Literature DB >> 21589465

Pyridine-2-carboximidamidate chloride monohydrate.

Qifan Chen, Huidong Zhang, Fang Zhang, Fei Liu.   

Abstract

The title compound, C(6)H(8)N(3) (+)·Cl(-)·H(2)O, crystallizes with three formula units in the asymmetric unit. The cations are non-planar with the -C(NH(2))(2) groups twisted out of the ring planes. Each pyridine carboximidamidate cation is linked to another cation through N-H⋯N hydrogen bonds, to chloride ions by N-H⋯Cl hydrogen bonds, and to water mol-ecules by N-H⋯O hydrogen bonds. Water mol-ecules and chloride ions are also linked together via O-H⋯Cl hydrogen bonds. In the crystal, all these inter-molecular inter-actions result in a three-dimensional network.

Entities:  

Year:  2010        PMID: 21589465      PMCID: PMC3011583          DOI: 10.1107/S1600536810046106

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


Related literature

For related structures, see: Guo et al. (2005 ▶); Fan et al. (2009 ▶); Góker et al. (2005 ▶); Walther et al. (2006 ▶).

Experimental

Crystal data

C6H8N3 +·Cl−·H2O M = 175.62 Triclinic, a = 7.2570 (15) Å b = 11.146 (2) Å c = 16.862 (3) Å α = 79.24 (3)° β = 82.14 (3)° γ = 78.34 (3)° V = 1305.3 (5) Å3 Z = 6 Mo Kα radiation μ = 0.39 mm−1 T = 293 K 0.25 × 0.24 × 0.22 mm

Data collection

Rigaku R-AXIS RAPID diffractometer Absorption correction: multi-scan (ABSCOR; Higashi, 1995 ▶) T min = 0.909, T max = 0.918 12872 measured reflections 5919 independent reflections 4550 reflections with I > 2σ(I) R int = 0.024

Refinement

R[F 2 > 2σ(F 2)] = 0.035 wR(F 2) = 0.117 S = 1.11 5919 reflections 418 parameters All H-atom parameters refined Δρmax = 0.23 e Å−3 Δρmin = −0.26 e Å−3 Data collection: RAPID-AUTO (Rigaku, 1998) ▶; cell refinement: RAPID-AUTO; data reduction: RAPID-AUTO; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: DIAMOND (Brandenburg, 1999 ▶) and SHELXP97 (Sheldrick, 2008 ▶); software used to prepare material for publication: SHELXL97. Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536810046106/zq2070sup1.cif Structure factors: contains datablocks I. DOI: 10.1107/S1600536810046106/zq2070Isup2.hkl Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C6H8N3+·Cl·H2OZ = 6
Mr = 175.62F(000) = 552
Triclinic, P1Dx = 1.340 Mg m3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 7.2570 (15) ÅCell parameters from 9445 reflections
b = 11.146 (2) Åθ = 3.0–27.4°
c = 16.862 (3) ŵ = 0.39 mm1
α = 79.24 (3)°T = 293 K
β = 82.14 (3)°Block, colourless
γ = 78.34 (3)°0.25 × 0.24 × 0.22 mm
V = 1305.3 (5) Å3
Rigaku R-AXIS RAPID diffractometer5919 independent reflections
Radiation source: fine-focus sealed tube4550 reflections with I > 2σ(I)
graphiteRint = 0.024
Detector resolution: 10 pixels mm-1θmax = 27.5°, θmin = 3.0°
ω scansh = −9→9
Absorption correction: multi-scan (ABSCOR; Higashi, 1995)k = −14→14
Tmin = 0.909, Tmax = 0.918l = −21→21
12872 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)] = 0.035Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.117All H-atom parameters refined
S = 1.11w = 1/[σ2(Fo2) + (0.0684P)2] where P = (Fo2 + 2Fc2)/3
5919 reflections(Δ/σ)max = 0.001
418 parametersΔρmax = 0.23 e Å3
0 restraintsΔρmin = −0.26 e Å3
Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'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 > 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
Cl10.17320 (7)0.30230 (4)0.10288 (2)0.04346 (13)
O10.7888 (3)0.60439 (14)0.40146 (10)0.0647 (4)
H1B0.690 (4)0.647 (3)0.4141 (15)0.073 (8)*
H100.821 (5)0.635 (3)0.344 (2)0.120 (11)*
N10.3062 (2)0.86483 (13)−0.07194 (8)0.0432 (3)
C10.3052 (3)0.98536 (18)−0.07462 (13)0.0540 (5)
H10.336 (4)1.031 (2)−0.1243 (15)0.078 (7)*
Cl20.13596 (7)0.30724 (4)−0.21061 (3)0.04888 (14)
O20.3482 (2)0.37193 (13)−0.07519 (9)0.0530 (4)
H0B0.305 (4)0.345 (2)−0.0273 (16)0.077 (8)*
H0A0.297 (4)0.351 (2)−0.1073 (17)0.075 (8)*
N20.1754 (2)0.60101 (14)0.06004 (10)0.0429 (3)
H2A0.111 (4)0.629 (2)0.1009 (15)0.071 (7)*
H2B0.180 (3)0.513 (2)0.0663 (12)0.053 (6)*
C20.2604 (3)1.04352 (17)−0.00802 (14)0.0561 (5)
H20.261 (3)1.131 (2)−0.0152 (12)0.055 (6)*
Cl30.43514 (7)0.80296 (4)0.45146 (3)0.05099 (14)
O30.4557 (3)0.86529 (14)0.26022 (10)0.0627 (4)
H03B0.561 (5)0.826 (3)0.2445 (19)0.102 (11)*
H03A0.448 (5)0.831 (3)0.316 (2)0.121 (12)*
N30.3540 (2)0.61884 (14)−0.06282 (9)0.0426 (3)
H3B0.410 (3)0.669 (2)−0.1007 (13)0.054 (6)*
H3A0.350 (3)0.544 (2)−0.0696 (12)0.051 (5)*
C30.2174 (3)0.97567 (18)0.06587 (13)0.0564 (5)
H30.189 (3)1.014 (2)0.1127 (14)0.070 (7)*
C40.2181 (3)0.85015 (18)0.07107 (11)0.0478 (4)
H40.192 (3)0.800 (2)0.1214 (14)0.067 (7)*
C50.2600 (2)0.80020 (14)0.00027 (9)0.0343 (3)
C60.2627 (2)0.66679 (14)−0.00077 (9)0.0338 (3)
N110.4303 (2)0.37190 (13)0.25233 (9)0.0428 (3)
C110.4055 (3)0.49449 (19)0.24780 (13)0.0540 (5)
H110.446 (3)0.542 (2)0.2001 (13)0.058 (6)*
N120.4363 (3)0.09814 (16)0.39452 (10)0.0502 (4)
H12B0.440 (3)0.014 (2)0.4040 (13)0.055 (6)*
H12A0.456 (3)0.128 (2)0.4371 (15)0.065 (7)*
C120.3223 (3)0.55573 (19)0.31194 (14)0.0604 (5)
H120.311 (4)0.648 (2)0.3024 (15)0.081 (8)*
N130.3872 (2)0.12940 (15)0.25963 (10)0.0447 (3)
H13B0.413 (3)0.045 (2)0.2600 (13)0.059 (6)*
H13A0.360 (3)0.187 (2)0.2153 (13)0.060 (6)*
C130.2613 (3)0.4879 (2)0.38308 (14)0.0599 (5)
H130.207 (4)0.528 (2)0.4224 (16)0.078 (8)*
C140.2851 (3)0.36072 (18)0.38966 (12)0.0477 (4)
H140.241 (3)0.3113 (19)0.4350 (12)0.048 (5)*
C150.3718 (2)0.30783 (15)0.32274 (10)0.0368 (3)
C160.4002 (2)0.17137 (16)0.32577 (10)0.0384 (4)
N21−0.0617 (2)0.10605 (13)0.39607 (8)0.0441 (3)
C21−0.0357 (3)−0.01675 (19)0.40054 (13)0.0563 (5)
H21−0.005 (3)−0.059 (2)0.4527 (13)0.062 (6)*
N22−0.0909 (2)0.38620 (15)0.25737 (9)0.0446 (3)
H22B−0.032 (3)0.359 (2)0.2128 (15)0.066 (7)*
H22A−0.111 (3)0.470 (2)0.2526 (14)0.069 (7)*
C22−0.0480 (3)−0.07293 (19)0.33556 (13)0.0559 (5)
H22−0.030 (3)−0.160 (2)0.3423 (13)0.061 (6)*
N23−0.2026 (2)0.35240 (16)0.39229 (10)0.0453 (4)
H23B−0.215 (3)0.430 (2)0.3963 (13)0.058 (6)*
H23A−0.232 (3)0.299 (2)0.4342 (14)0.057 (6)*
C23−0.0891 (3)−0.00047 (19)0.26314 (12)0.0526 (5)
H23−0.103 (4)−0.035 (2)0.2163 (15)0.077 (7)*
C24−0.1160 (3)0.12748 (18)0.25641 (10)0.0431 (4)
H24−0.146 (3)0.1764 (18)0.2077 (12)0.048 (5)*
C25−0.1009 (2)0.17539 (15)0.32452 (9)0.0338 (3)
C26−0.1327 (2)0.31196 (15)0.32427 (9)0.0352 (3)
U11U22U33U12U13U23
Cl10.0579 (3)0.0378 (2)0.0333 (2)−0.01169 (18)0.00298 (17)−0.00477 (16)
O10.0845 (12)0.0469 (8)0.0521 (9)0.0040 (8)0.0066 (8)−0.0091 (7)
N10.0551 (9)0.0372 (8)0.0361 (7)−0.0117 (7)−0.0026 (6)−0.0009 (6)
C10.0739 (14)0.0379 (10)0.0502 (11)−0.0197 (9)−0.0090 (10)0.0050 (9)
Cl20.0640 (3)0.0430 (2)0.0393 (2)−0.0127 (2)0.00567 (19)−0.01046 (18)
O20.0740 (10)0.0492 (8)0.0412 (7)−0.0272 (7)0.0026 (7)−0.0098 (6)
N20.0535 (9)0.0310 (7)0.0428 (8)−0.0122 (7)0.0073 (7)−0.0061 (6)
C20.0651 (13)0.0295 (9)0.0749 (14)−0.0119 (8)−0.0056 (11)−0.0094 (9)
Cl30.0642 (3)0.0439 (2)0.0370 (2)−0.0035 (2)0.00486 (19)−0.00088 (18)
O30.0851 (12)0.0472 (8)0.0474 (8)−0.0042 (8)0.0026 (8)−0.0020 (7)
N30.0529 (9)0.0337 (8)0.0407 (8)−0.0116 (7)0.0084 (7)−0.0102 (7)
C30.0654 (13)0.0476 (11)0.0625 (12)−0.0181 (10)0.0094 (10)−0.0280 (10)
C40.0608 (12)0.0435 (10)0.0397 (9)−0.0164 (9)0.0071 (8)−0.0098 (8)
C50.0341 (8)0.0301 (8)0.0375 (8)−0.0047 (6)−0.0016 (6)−0.0056 (6)
C60.0351 (8)0.0304 (8)0.0346 (8)−0.0056 (6)−0.0029 (6)−0.0032 (6)
N110.0463 (8)0.0403 (8)0.0413 (8)−0.0133 (7)−0.0022 (6)−0.0011 (6)
C110.0637 (13)0.0431 (10)0.0535 (11)−0.0168 (9)−0.0050 (10)0.0036 (9)
N120.0662 (11)0.0378 (9)0.0454 (9)−0.0115 (8)−0.0133 (8)0.0036 (7)
C120.0682 (14)0.0369 (10)0.0749 (15)−0.0044 (9)−0.0132 (11)−0.0077 (10)
N130.0533 (9)0.0357 (8)0.0439 (8)−0.0081 (7)−0.0068 (7)−0.0020 (7)
C130.0672 (14)0.0520 (12)0.0582 (12)0.0050 (10)−0.0078 (11)−0.0191 (10)
C140.0487 (10)0.0482 (10)0.0398 (9)−0.0024 (8)−0.0011 (8)−0.0003 (8)
C150.0332 (8)0.0374 (9)0.0389 (8)−0.0072 (7)−0.0064 (7)−0.0013 (7)
C160.0322 (8)0.0416 (9)0.0394 (8)−0.0090 (7)−0.0025 (7)0.0000 (7)
N210.0555 (9)0.0392 (8)0.0350 (7)−0.0006 (7)−0.0085 (6)−0.0053 (6)
C210.0746 (14)0.0421 (10)0.0474 (10)0.0028 (9)−0.0149 (10)−0.0041 (8)
N220.0531 (9)0.0370 (8)0.0395 (8)−0.0089 (7)0.0081 (7)−0.0044 (7)
C220.0681 (14)0.0391 (10)0.0615 (12)−0.0083 (9)−0.0054 (10)−0.0137 (9)
N230.0547 (10)0.0402 (9)0.0387 (8)−0.0099 (7)0.0087 (7)−0.0088 (7)
C230.0634 (13)0.0548 (11)0.0470 (10)−0.0201 (10)−0.0012 (9)−0.0202 (9)
C240.0499 (10)0.0495 (10)0.0328 (8)−0.0184 (8)−0.0036 (7)−0.0046 (7)
C250.0287 (7)0.0381 (8)0.0337 (7)−0.0066 (6)0.0006 (6)−0.0060 (6)
C260.0309 (8)0.0383 (9)0.0355 (8)−0.0074 (7)0.0001 (6)−0.0053 (7)
O1—H1B0.80 (3)N12—H12A0.89 (2)
O1—H100.98 (4)C12—C131.363 (3)
N1—C51.331 (2)C12—H121.00 (3)
N1—C11.334 (2)N13—C161.309 (2)
C1—C21.369 (3)N13—H13B0.92 (2)
C1—H10.92 (2)N13—H13A0.91 (2)
O2—H0B0.85 (3)C13—C141.378 (3)
O2—H0A0.79 (3)C13—H130.87 (3)
N2—C61.311 (2)C14—C151.386 (3)
N2—H2A0.85 (3)C14—H140.91 (2)
N2—H2B0.96 (2)C15—C161.485 (2)
C2—C31.364 (3)N21—C211.333 (2)
C2—H20.96 (2)N21—C251.338 (2)
O3—H03B0.84 (4)C21—C221.381 (3)
O3—H03A0.94 (4)C21—H210.95 (2)
N3—C61.302 (2)N22—C261.307 (2)
N3—H3B0.88 (2)N22—H22B0.89 (3)
N3—H3A0.87 (2)N22—H22A0.91 (2)
C3—C41.384 (3)C22—C231.366 (3)
C3—H30.95 (2)C22—H220.94 (2)
C4—C51.381 (2)N23—C261.311 (2)
C4—H40.94 (2)N23—H23B0.87 (2)
C5—C61.486 (2)N23—H23A0.87 (2)
N11—C151.330 (2)C23—C241.385 (3)
N11—C111.331 (2)C23—H230.97 (2)
C11—C121.390 (3)C24—C251.380 (2)
C11—H110.92 (2)C24—H240.924 (19)
N12—C161.312 (2)C25—C261.492 (2)
N12—H12B0.91 (2)
H1B—O1—H10106 (3)C16—N13—H13A116.6 (13)
C5—N1—C1116.70 (15)H13B—N13—H13A124.4 (19)
N1—C1—C2123.59 (18)C12—C13—C14119.3 (2)
N1—C1—H1117.3 (16)C12—C13—H13117.7 (17)
C2—C1—H1119.1 (16)C14—C13—H13123.0 (17)
H0B—O2—H0A111 (2)C13—C14—C15117.69 (19)
C6—N2—H2A125.2 (16)C13—C14—H14122.7 (13)
C6—N2—H2B124.9 (13)C15—C14—H14119.5 (12)
H2A—N2—H2B110 (2)N11—C15—C14124.30 (16)
C3—C2—C1119.11 (17)N11—C15—C16115.39 (15)
C3—C2—H2122.4 (12)C14—C15—C16120.29 (16)
C1—C2—H2118.5 (12)N13—C16—N12122.82 (17)
H03B—O3—H03A100 (3)N13—C16—C15118.41 (15)
C6—N3—H3B116.3 (14)N12—C16—C15118.77 (16)
C6—N3—H3A122.4 (14)C21—N21—C25116.99 (15)
H3B—N3—H3A120.9 (19)N21—C21—C22122.95 (18)
C2—C3—C4118.91 (18)N21—C21—H21111.6 (13)
C2—C3—H3120.1 (14)C22—C21—H21125.4 (13)
C4—C3—H3121.0 (14)C26—N22—H22B123.0 (15)
C5—C4—C3117.91 (18)C26—N22—H22A124.0 (15)
C5—C4—H4121.0 (13)H22B—N22—H22A113 (2)
C3—C4—H4121.1 (13)C23—C22—C21119.16 (18)
N1—C5—C4123.74 (15)C23—C22—H22121.3 (13)
N1—C5—C6114.14 (13)C21—C22—H22119.5 (13)
C4—C5—C6122.09 (15)C26—N23—H23B121.2 (15)
N3—C6—N2122.05 (15)C26—N23—H23A118.2 (14)
N3—C6—C5118.14 (15)H23B—N23—H23A121 (2)
N2—C6—C5119.81 (15)C22—C23—C24119.30 (17)
C15—N11—C11116.63 (16)C22—C23—H23122.4 (15)
N11—C11—C12123.22 (19)C24—C23—H23118.3 (15)
N11—C11—H11119.1 (14)C25—C24—C23117.51 (17)
C12—C11—H11117.7 (14)C25—C24—H24123.3 (12)
C16—N12—H12B124.8 (13)C23—C24—H24119.2 (12)
C16—N12—H12A121.0 (15)N21—C25—C24124.10 (15)
H12B—N12—H12A114.1 (19)N21—C25—C26114.20 (14)
C13—C12—C11118.88 (19)C24—C25—C26121.68 (15)
C13—C12—H12124.1 (15)N22—C26—N23122.63 (16)
C11—C12—H12117.0 (15)N22—C26—C25119.59 (15)
C16—N13—H13B119.0 (13)N23—C26—C25117.78 (15)
D—H···AD—HH···AD···AD—H···A
N23—H23B···O1i0.87 (2)1.97 (2)2.829 (2)173 (2)
N22—H22B···Cl10.89 (3)2.31 (3)3.187 (2)169 (2)
N12—H12B···Cl3ii0.91 (2)2.35 (2)3.2522 (19)170.2 (18)
O1—H1B···Cl30.80 (3)2.37 (3)3.163 (2)169 (2)
N2—H2A···Cl2iii0.85 (3)2.49 (3)3.326 (2)167 (2)
O1—H10···Cl2iv0.98 (4)2.22 (4)3.1902 (19)173 (3)
N3—H3A···O20.87 (2)1.94 (2)2.808 (2)174.9 (19)
N2—H2B···Cl10.96 (2)2.32 (2)3.2754 (17)170.9 (17)
N12—H12A···Cl3v0.89 (2)2.43 (2)3.313 (2)171 (2)
N23—H23A···Cl3vi0.87 (2)2.50 (2)3.324 (2)158 (2)
N13—H13B···O3ii0.92 (2)1.97 (2)2.883 (2)178 (2)
N22—H22A···Cl2iii0.91 (2)2.43 (3)3.3194 (18)168 (2)
N13—H13A···Cl10.91 (2)2.48 (2)3.335 (2)156.9 (19)
O3—H03B···Cl2iv0.84 (4)2.45 (4)3.286 (2)174 (3)
O2—H0B···Cl10.85 (3)2.28 (3)3.1171 (18)172 (2)
O2—H0A···Cl20.79 (3)2.40 (3)3.1833 (18)175 (3)
O3—H03A···Cl30.94 (4)2.25 (4)3.1586 (18)164 (3)
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯AD—HH⋯ADAD—H⋯A
N23—H23B⋯O1i0.87 (2)1.97 (2)2.829 (2)173 (2)
N22—H22B⋯Cl10.89 (3)2.31 (3)3.187 (2)169 (2)
N12—H12B⋯Cl3ii0.91 (2)2.35 (2)3.2522 (19)170.2 (18)
O1—H1B⋯Cl30.80 (3)2.37 (3)3.163 (2)169 (2)
N2—H2A⋯Cl2iii0.85 (3)2.49 (3)3.326 (2)167 (2)
O1—H10⋯Cl2iv0.98 (4)2.22 (4)3.1902 (19)173 (3)
N3—H3A⋯O20.87 (2)1.94 (2)2.808 (2)174.9 (19)
N2—H2B⋯Cl10.96 (2)2.32 (2)3.2754 (17)170.9 (17)
N12—H12A⋯Cl3v0.89 (2)2.43 (2)3.313 (2)171 (2)
N23—H23A⋯Cl3vi0.87 (2)2.50 (2)3.324 (2)158 (2)
N13—H13B⋯O3ii0.92 (2)1.97 (2)2.883 (2)178 (2)
N22—H22A⋯Cl2iii0.91 (2)2.43 (3)3.3194 (18)168 (2)
N13—H13A⋯Cl10.91 (2)2.48 (2)3.335 (2)156.9 (19)
O3—H03B⋯Cl2iv0.84 (4)2.45 (4)3.286 (2)174 (3)
O2—H0B⋯Cl10.85 (3)2.28 (3)3.1171 (18)172 (2)
O2—H0A⋯Cl20.79 (3)2.40 (3)3.1833 (18)175 (3)
O3—H03A⋯Cl30.94 (4)2.25 (4)3.1586 (18)164 (3)

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

  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.  Synthesis and potent antibacterial activity against MRSA of some novel 1,2-disubstituted-1H-benzimidazole-N-alkylated-5-carboxamidines.

Authors:  Hakan Göker; Seçkin Ozden; Sulhiye Yildiz; David W Boykin
Journal:  Eur J Med Chem       Date:  2005-06-29       Impact factor: 6.514

3.  Synthesis of azolyl carboximidamides as ligands for Zn(II) and Cu(II): application of the Zn(II) complexes as catalysts for the copolymerization of carbon dioxide and epoxides.

Authors:  Martin Walther; Kurt Wermann; Marion Lutsche; Wolfgang Günther; Helmar Görls; Ernst Anders
Journal:  J Org Chem       Date:  2006-02-17       Impact factor: 4.354

4.  Pyridine-4-carboximidamidate chloride.

Authors:  Ping Fan; Lei Wang; Huidong Zhang
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2009-09-09
  4 in total
  1 in total

1.  Pyridine-3-carboxamidinium chloride.

Authors:  Fei Liu; Fang Zhang; Qifan Chen; Huidong Zhang
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2011-03-05
  1 in total

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