Literature DB >> 21754444

Pyridine-4-carbaldehyde 4-phenylsemicarbazone.

Rafael Mendoza-Meroño1, Laura Menéndez-Taboada, Eva Fernández-Zapico, Santiago García-Granda.   

Abstract

In the title compound, C(13)H(12)N(4)O, the semicarbazone fragment links a benzene and a pyridine ring in the structure. The crystal packing is stabilized by strong inter-molecular N-H⋯O hydrogen bonds, which connect two mol-ecules to form a synthon unit, and by N-H⋯N hydrogen bonds and weak C-H⋯π inter-actions. The mol-ecular conformation is stabil-ized by intra-molecular N-H⋯N and C-H⋯O inter-actions.

Entities:  

Year:  2011        PMID: 21754444      PMCID: PMC3089140          DOI: 10.1107/S1600536811013134

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


Related literature

For related compounds and their biological activity, see: Pavan et al. (2010 ▶); Yogeeswari et al. (2005 ▶).

Experimental

Crystal data

C13H12N4O M = 240.27 Monoclinic, a = 9.2794 (6) Å b = 10.3384 (8) Å c = 12.8244 (8) Å β = 100.744 (6)° V = 1208.73 (15) Å3 Z = 4 Cu Kα radiation μ = 0.72 mm−1 T = 295 K 0.30 × 0.11 × 0.06 mm

Data collection

Oxford Diffraction Xcalibur Gemini R diffractometer Absorption correction: multi-scan (ABSPACK in CrysAlis PRO; Oxford Diffraction, 2010 ▶) T min = 0.888, T max = 1.000 7257 measured reflections 2310 independent reflections 1702 reflections with I > 2σ(I) R int = 0.066

Refinement

R[F 2 > 2σ(F 2)] = 0.052 wR(F 2) = 0.143 S = 1.06 2310 reflections 176 parameters H atoms treated by a mixture of independent and constrained refinement Δρmax = 0.20 e Å−3 Δρmin = −0.17 e Å−3 Data collection: CrysAlis CCD (Oxford Diffraction, 2010 ▶); cell refinement: CrysAlis RED (Oxford Diffraction, 2010 ▶); data reduction: CrysAlis RED; program(s) used to solve structure: SIR92 (Altomare et al., 1994 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997 ▶) and Mercury (Macrae et al., 2008 ▶); software used to prepare material for publication: WinGX publication routines (Farrugia, 1999 ▶), PLATON (Spek, 2009) ▶ and PARST95 (Nardelli, 1995 ▶). Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536811013134/fy2007sup1.cif Structure factors: contains datablocks I. DOI: 10.1107/S1600536811013134/fy2007Isup2.hkl Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C13H12N4OF(000) = 504
Mr = 240.27Dx = 1.320 Mg m3
Monoclinic, P21/cMelting point: 493.15 K
Hall symbol: -P 2ybcCu Kα radiation, λ = 1.54180 Å
a = 9.2794 (6) ÅCell parameters from 2114 reflections
b = 10.3384 (8) Åθ = 3.5–70.7°
c = 12.8244 (8) ŵ = 0.72 mm1
β = 100.744 (6)°T = 295 K
V = 1208.73 (15) Å3Rod, white
Z = 40.30 × 0.11 × 0.06 mm
Oxford Diffraction Xcalibur Gemini R diffractometer2310 independent reflections
Radiation source: Enhance (Cu) X-ray Source1702 reflections with I > 2σ(I)
graphiteRint = 0.066
Detector resolution: 10.2673 pixels mm-1θmax = 70.8°, θmin = 4.9°
ω scansh = −10→11
Absorption correction: multi-scan (ABSPACK in CrysAlis PRO; Oxford Diffraction, 2010)k = −12→11
Tmin = 0.888, Tmax = 1.000l = −15→15
7257 measured reflections
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.052H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.143w = 1/[σ2(Fo2) + (0.0648P)2 + 0.0647P] where P = (Fo2 + 2Fc2)/3
S = 1.06(Δ/σ)max < 0.001
2310 reflectionsΔρmax = 0.20 e Å3
176 parametersΔρmin = −0.17 e Å3
0 restraintsExtinction correction: SHELXL, Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.0051 (8)
Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds 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 > 2sigma(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
O10.31018 (14)0.04113 (16)0.96710 (10)0.0562 (4)
N20.47959 (17)−0.03751 (17)0.75432 (12)0.0474 (4)
N30.45910 (18)−0.01377 (19)0.85540 (13)0.0524 (5)
N40.23363 (17)0.07764 (18)0.78923 (13)0.0478 (4)
N10.7010 (2)−0.1407 (2)0.43544 (14)0.0619 (5)
C70.3301 (2)0.0358 (2)0.87508 (14)0.0443 (5)
C40.5324 (2)−0.1475 (2)0.55575 (16)0.0505 (5)
H40.4383−0.16660.56650.061*
C30.5689 (2)−0.1643 (2)0.45723 (16)0.0557 (5)
H30.4964−0.19400.40240.067*
C80.0926 (2)0.1288 (2)0.79070 (15)0.0467 (5)
C50.6378 (2)−0.1016 (2)0.63847 (15)0.0466 (5)
C90.0279 (2)0.2034 (2)0.70528 (16)0.0551 (5)
H90.07820.21930.65020.066*
C60.6074 (2)−0.0739 (2)0.74389 (16)0.0489 (5)
C130.0161 (2)0.1054 (2)0.87145 (16)0.0575 (6)
H130.05720.05410.92890.069*
C10−0.1102 (3)0.2545 (3)0.70086 (19)0.0672 (7)
H10−0.15280.30380.64250.081*
C20.8014 (2)−0.0989 (3)0.51620 (18)0.0657 (6)
H20.8949−0.08170.50340.079*
C10.7765 (2)−0.0794 (2)0.61736 (17)0.0571 (6)
H10.8519−0.05160.67090.069*
C12−0.1218 (2)0.1586 (3)0.86654 (19)0.0687 (7)
H12−0.17220.14340.92160.082*
C11−0.1858 (3)0.2335 (3)0.7820 (2)0.0712 (7)
H11−0.27830.26920.77960.085*
H60.686 (2)−0.083 (2)0.8069 (17)0.058 (6)*
H3N0.533 (3)−0.031 (2)0.9132 (19)0.065 (7)*
H4N0.266 (2)0.080 (2)0.7265 (18)0.053 (6)*
U11U22U33U12U13U23
O10.0482 (8)0.0824 (11)0.0385 (7)0.0050 (7)0.0096 (6)−0.0017 (7)
N20.0489 (9)0.0571 (10)0.0367 (8)0.0029 (7)0.0089 (7)−0.0020 (7)
N30.0444 (9)0.0765 (13)0.0358 (8)0.0107 (8)0.0066 (7)−0.0017 (8)
N40.0439 (9)0.0619 (11)0.0388 (8)0.0066 (7)0.0110 (7)0.0011 (7)
N10.0681 (12)0.0707 (13)0.0507 (10)0.0103 (9)0.0212 (9)0.0032 (9)
C70.0430 (10)0.0525 (12)0.0373 (10)−0.0012 (8)0.0076 (7)−0.0035 (8)
C40.0517 (11)0.0529 (12)0.0482 (11)0.0021 (9)0.0124 (9)−0.0005 (9)
C30.0614 (13)0.0577 (14)0.0473 (12)0.0047 (10)0.0081 (9)−0.0026 (9)
C80.0447 (10)0.0521 (12)0.0437 (10)0.0019 (8)0.0092 (8)−0.0038 (8)
C50.0484 (10)0.0497 (12)0.0423 (10)0.0084 (8)0.0103 (8)0.0044 (8)
C90.0580 (12)0.0613 (14)0.0472 (11)0.0101 (10)0.0127 (9)0.0036 (10)
C60.0430 (10)0.0603 (13)0.0428 (10)0.0061 (9)0.0065 (8)0.0024 (9)
C130.0521 (11)0.0751 (16)0.0479 (11)0.0077 (10)0.0159 (9)0.0106 (10)
C100.0679 (14)0.0759 (17)0.0579 (14)0.0233 (11)0.0116 (11)0.0102 (11)
C20.0568 (13)0.0857 (18)0.0597 (13)0.0021 (11)0.0239 (11)0.0007 (12)
C10.0464 (11)0.0726 (15)0.0530 (12)0.0040 (10)0.0105 (9)−0.0012 (10)
C120.0568 (13)0.0924 (19)0.0611 (14)0.0139 (12)0.0219 (10)0.0058 (13)
C110.0586 (14)0.0851 (19)0.0725 (16)0.0239 (12)0.0193 (12)0.0045 (13)
O1—C71.229 (2)C8—C91.382 (3)
N2—C61.275 (2)C5—C11.383 (3)
N2—N31.367 (2)C5—C61.460 (3)
N3—N21.367 (2)C9—C101.378 (3)
N3—C71.368 (2)C9—H90.9300
N3—H3N0.93 (2)C6—H60.99 (2)
N4—C71.354 (2)C13—C121.384 (3)
N4—C81.415 (2)C13—H130.9300
N4—H4N0.91 (2)C10—C111.376 (3)
N1—C31.329 (3)C10—H100.9300
N1—C21.329 (3)C2—C11.374 (3)
C4—C31.379 (3)C2—H20.9300
C4—C51.386 (3)C1—H10.9300
C4—H40.9300C12—C111.373 (3)
C3—H30.9300C12—H120.9300
C8—C131.381 (3)C11—H110.9300
C6—N2—N3116.68 (16)C10—C9—H9119.7
N2—N3—C7121.56 (16)C8—C9—H9119.7
N2—N3—H3N120.5 (14)N2—C6—C5119.94 (17)
C7—N3—H3N117.9 (14)N2—C6—H6120.3 (12)
C7—N4—C8125.56 (16)C5—C6—H6119.8 (12)
C7—N4—H4N116.7 (13)C8—C13—C12119.8 (2)
C8—N4—H4N117.4 (13)C8—C13—H13120.1
C3—N1—C2115.80 (18)C12—C13—H13120.1
O1—C7—N4124.85 (17)C11—C10—C9120.6 (2)
O1—C7—N3119.15 (17)C11—C10—H10119.7
N4—C7—N3115.99 (16)C9—C10—H10119.7
C3—C4—C5119.03 (19)N1—C2—C1124.5 (2)
C3—C4—H4120.5N1—C2—H2117.7
N1—C3—C4124.3 (2)C1—C2—H2117.7
N1—C3—H3117.9C2—C1—C5119.1 (2)
C4—C3—H3117.9C2—C1—H1120.4
C13—C8—C9118.96 (18)C5—C1—H1120.4
C13—C8—N4123.37 (18)C11—C12—C13121.3 (2)
C9—C8—N4117.65 (18)C11—C12—H12119.3
C1—C5—C4117.19 (18)C13—C12—H12119.3
C1—C5—C6119.74 (18)C12—C11—C10118.7 (2)
C4—C5—C6123.05 (18)C12—C11—H11120.7
C10—C9—C8120.6 (2)C10—C11—H11120.7
C6—N2—N3—C7174.5 (2)N3—N2—C6—C5179.75 (18)
C8—N4—C7—O1−2.8 (3)C1—C5—C6—N2148.6 (2)
C8—N4—C7—N3178.13 (19)C4—C5—C6—N2−30.0 (3)
N2—N3—C7—O1171.39 (19)C9—C8—C13—C12−1.2 (3)
N2—N3—C7—N4−9.5 (3)N4—C8—C13—C12−179.6 (2)
C2—N1—C3—C40.3 (3)C8—C9—C10—C110.7 (4)
C5—C4—C3—N10.8 (3)C3—N1—C2—C1−0.1 (4)
C7—N4—C8—C13−21.7 (3)N1—C2—C1—C5−1.3 (4)
C7—N4—C8—C9159.8 (2)C4—C5—C1—C22.3 (3)
C3—C4—C5—C1−2.1 (3)C6—C5—C1—C2−176.3 (2)
C3—C4—C5—C6176.49 (19)C8—C13—C12—C110.8 (4)
C13—C8—C9—C100.4 (3)C13—C12—C11—C100.3 (4)
N4—C8—C9—C10179.0 (2)C9—C10—C11—C12−1.1 (4)
Cg2 is the centroid of the C8–C13 ring.
D—H···AD—HH···AD···AD—H···A
N3—H3N···O1i0.93 (2)1.91 (2)2.833 (2)172 (2)
N4—H4N···N1ii0.91 (2)2.24 (2)3.122 (3)161.8 (19)
N4—H4N···N20.91 (2)2.29 (2)2.685 (2)105.4 (16)
C13—H13···O10.932.312.854 (2)117
C1—H1···Cg2iii0.932.883.644 (2)140
Table 1

Hydrogen-bond geometry (Å, °)

Cg2 is the centroid of the C8–C13 ring.

D—H⋯AD—HH⋯ADAD—H⋯A
N3—H3N⋯O1i0.93 (2)1.91 (2)2.833 (2)172 (2)
N4—H4N⋯N1ii0.91 (2)2.24 (2)3.122 (3)161.8 (19)
N4—H4N⋯N20.91 (2)2.29 (2)2.685 (2)105.4 (16)
C13—H13⋯O10.932.312.854 (2)117
C1—H1⋯Cg2iii0.932.883.644 (2)140

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.  Thiosemicarbazones, semicarbazones, dithiocarbazates and hydrazide/hydrazones: anti-Mycobacterium tuberculosis activity and cytotoxicity.

Authors:  Fernando R Pavan; Pedro I da S Maia; Sergio R A Leite; Victor M Deflon; Alzir A Batista; Daisy N Sato; Scott G Franzblau; Clarice Q F Leite
Journal:  Eur J Med Chem       Date:  2010-01-28       Impact factor: 6.514

3.  Synthesis of aryl semicarbazones as potential anticonvulsant agents.

Authors:  P Yogeeswari; D Sriram; V Veena; R Kavya; K Rakhra; J Vaigunda Ragavendran; S Mehta; R Thirumurugan; J P Stables
Journal:  Biomed Pharmacother       Date:  2005-01-26       Impact factor: 6.529

4.  Structure validation in chemical crystallography.

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

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