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Acta Crystallographica Section E: Crystallographic Communications logoLink to Acta Crystallographica Section E: Crystallographic Communications
. 2015 Jan 17;71(Pt 2):168–172. doi: 10.1107/S2056989015000663

Crystal structures of crotonaldehyde semicarbazone and crotonaldehyde thiosemicarbazone from X-ray powder diffraction data

Atef Arfan a, Mwaffak Rukiah a,*
PMCID: PMC4384554  PMID: 25878810

Crotonaldehyde semicarbazone and crotonaldehyde thio­semicarbazone show the same E conformation around the imine C=N bond. Each mol­ecule has an intra­molecular N—H⋯N hydrogen bond, which generates an S(5) ring. Inter­molecular N—H⋯O hydrogen bonds in the semicarbazone link the mol­ecules into layers parallel to the bc plane, while weak inter­molecular N—H⋯S hydrogen bonds in the thio­semicarbazone link the mol­ecules into chains propagating in [110].

Keywords: crystal structure, crotonaldehyde, semicarbazone, thio­semicarbazone, powder X-ray diffraction, supra­molecular structure, hydrogen bond, one-dimensional chain, two-dimensional networks

Abstract

Crotonaldehyde semicarbazone {systematic name: (E)-2-[(E)-but-2-en-1-yl­idene]hydrazinecarboxamide}, C5H9N3O, (I), and crotonaldehyde thio­semi­carba­zone {systematic name: (E)-2-[(E)-but-2-en-1-yldene]hydra­zinecarbo­­thio­amide}, C5H9N3S, (II), show the same E conformation around the imine C=N bond. Compounds (I) and (II) were obtained by the condensation of crotonaldehyde with semicarbazide hydro­chloride and thio­semicarbazide, respectively. Each mol­ecule has an intra­molecular N—H⋯N hydrogen bond, which generates an S(5) ring. In (I), the crotonaldehyde fragment is twisted by 2.59 (5)° from the semicarbazide mean plane, while in (II) the corresponding angle (with the thio­semicarbazide mean plane) is 9.12 (5)°. The crystal packing is different in the two compounds: in (I) inter­molecular N—H⋯O hydrogen bonds link the mol­ecules into layers parallel to the bc plane, while weak inter­molecular N—H⋯S hydrogen bonds in (II) link the mol­ecules into chains propagating in [110].

Chemical context  

The chemistry of semicarbazones and thio­semicarbazones is especially inter­esting due to their special role in biological applications such as anti-proliferative, anti-tumoral, anti-convulsant, anti-trypanosomal, herbicidal and biocidal activities (Beraldo et al., 2002 ▸; Kasuga et al., 2003 ▸; Teixeira et al., 2003 ▸; Beraldo & Gambino, 2004 ▸; Mikhaleva et al., 2008 ▸; de Oliveira et al., 2008 ▸; Alomar et al., 2012 ▸; Gan et al., 2014 ▸). They are also important inter­mediates in organic synthesis, mainly for obtaining heterocyclic rings, such as thia­zolidones, oxa­diazo­les, pyrazolidones, and thia­diazo­les (Greenbaum et al., 2004 ▸; Küçükgüzel et al., 2006 ▸). Semicarbazones and thio­semicarbazones have received considerable attention in view of their simplicity of preparation, various complexing abilities and coordination behavior that can be used in analytical applications (Garg & Jain, 1988 ▸; Casas et al., 2000 ▸). They are of inter­est from a supra­molecular point of view since they can be functionalized to give different supra­molecular arrays.graphic file with name e-71-00168-scheme1.jpg

Structural commentary  

Compounds (I) and (II) crystallize in centrosymmetric space groups P21/c and P Inline graphic, respectively, with one mol­ecule in the asymmetric unit. Each mol­ecule has an intra­molecular N—H⋯N hydrogen bond (Tables 1 ▸ and 2 ▸), which forms an S(5) ring. The semicarbazone and thio­semicarbazone fragments in the compounds show an E conformation around the imine C=N bond. The mol­ecules (Fig. 1 ▸) are approximately planar, with a dihedral angle of 2.59 (5)° between the C1/C2/C3 crotonaldehyde plane and the mean plane of the C4/N1/N2/C5/O1/N3 semicarbazone fragment for (I), and of 9.12 (5)° between the C1/C2/C3 crotonaldehyde plane and the mean plane of the C4/N1/N2/C5/S1/N3 thio­semicarbazone fragment for (II). All bond lengths and angles in (I) and (II) are normal and correspond well to those observed in the crystal structures of related semi- and thio­semicarbazone derivatives, viz. acetone semicarbazone and benzaldehyde­semicarbazone (Naik & Palenik, 1974 ▸), 3,4- methyl­ene­dioxy­benzaldehyde­semicarbazone (Wang et al., 2004 ▸), isatin 3-semicarbazone and 1-methyl­isatin 3-semicarbazone (Pelosi et al., 2005 ▸), 4- (methyl­sulfan­yl)benzaldehyde­thio­semicarbazone (Yathirajan et al., 2006 ▸), 4-(methyl­sulfan­yl)benzaldehyde­semicarbazone (Sarojini et al., 2007 ▸), 5-hy­droxy-2-nitro­benzaldehyde thio­semicarbazone (Reddy et al., 2014 ▸) and 1-(4-formyl­benzyl­idene) thio­semicarbazone (Carballo et al., 2014 ▸).

Table 1. Hydrogen-bond geometry (, ) for (I) .

DHA DH HA D A DHA
N3H2N3N1 0.87 2.33 2.629(19) 100
N2H1N2O1i 0.88 2.07 2.910(11) 158
N3H1N3O1ii 0.91 2.04 2.914(18) 162
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Symmetry codes: (i) Inline graphic; (ii) Inline graphic.

Table 2. Hydrogen-bond geometry (, ) for (II) .

DHA DH HA D A DHA
N3H2N3N1 0.89 2.17 2.641(14) 112
N2H1N2S1i 0.86 2.83 3.473(11) 133
N3H1N3S1ii 0.87 2.77 3.398(11) 130
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Symmetry codes: (i) Inline graphic; (ii) Inline graphic.

Figure 1.

Figure 1

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The mol­ecular structures of (a) (I) and (b) (II), showing the atom-labelling schemes. Displacement spheres (and the ellipsoid for S1) are drawn at the 50% probability level.

Supra­molecular features  

As a result of the presence of potential hydrogen-donor sites in mol­ecules (I) and (II), supra­molecular hydrogen-bonding inter­actions are observed in both compounds (Tables 1 ▸ and 2 ▸). In the crystal of (I), mol­ecules are linked by pairs of N—H⋯O hydrogen bonds, forming inversion dimers with R22(8) ring motifs (Fig. 2 ▸ a). The resulting dimers are connected through N—H⋯O hydrogen bonds, forming layers parallel to bc plane. In the crystal of (II), mol­ecules are linked by weak N—H⋯S hydrogen bonds, forming chains propagating in [110] (Fig. 2 ▸ b).

Figure 2.

Figure 2

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(a) A portion of the crystal packing of (I) viewed down the b axis (parallel to the hydrogen-bonded layer). (b) A portion of the crystal packing of (II), showing the hydrogen-bonded chain of the mol­ecules. Thin dotted lines denote inter­molecular hydrogen bonds.

Synthesis and crystallization  

All reactions and manipulations were carried out in air with reagent grade solvents. The IR spectra were recorded on a Jasco FT–IR 300E instrument. 1H and 13C{1H} NMR spectra were recorded on a Bruker Bio spin 400 spectrometer. Microanalysis was performed using EURO EA. Powder X-ray diffraction data were collected with Stoe Transmission diffractometer (Stadi P).

For the synthesis of (I), a mixture of semicarbazide hydro­chloride (CH5N3O·HCl; 0.5 g, 4.5 mmol) and sodium acetate (CH3COONa; 0.75 g, 9.1 mmol) in 10 ml water was agitated well and crotonaldehyde (0.5 g, 7.1 mmol) was added slowly with stirring. On completion of the addition, the reaction mixture was agitated for 24 h at room temperature. The solid product which formed was separated by filtration and washed with water and finally recrystallized from absolute ethanol to produce the product (I) (white powder; m.p. 481–482 K) in 55.5% yield.

IR (KBr, ν, cm−1): 3456, 3281, 3192 (NH2), (1668–1638) (C=O); 1H NMR (400 MHz, CD3OD) δ p.p.m. 1.76 (d, J = 4.42 Hz, 3H, –CH3), 6.43–5.46 (m, 2H, –HC=CH–), 7.39 (d, J = 7.19 Hz, 1H, HC=N–).13C NMR (100 MHz, CD3OD) δ p.p.m. 18.52 (CH3), 130.01 (–HC=CH–), 137.62 (–HC=CH–), 145.64 (N=C), 160.19 (C=O). Analysis calculated for (I): C, 47.23; H, 7.13; N, 33.05, 12.58 O%. Found: C, 46.43; H, 6.08; N, 34.69%

For the synthesis of (II), crotonaldehyde (0.5 g, 7.1 mmol) was added to thio­semicarbazide (CH5N3S; 0.65 g, 7.1 mmol) in 5 ml water and the mixture was stirred at room temperature for 24 h. The product was separated by filtration and recrystallized from absolute ethanol to produce the product (II) (white powder; m.p. 435–436 K) in 72.5% yield.

IR (KBr, ν, cm−1): 3323, 3244, 3164 (NH2), 1650(C=S). 1H NMR (400 MHz, CDCl3) δ p.p.m. 1.90 (d, J = 5.86 Hz, 3H, –CH3), 6.07–6.27 (m, 2H, –HC=CH–), 6.49 (sb, 1H), 7.10 (sb, 1H) 7.60 (d, J = 8.57 Hz, 1H, HC=N–), 10.10 (sb, 2H). 13C NMR (100.6 MHz, CDCl3) 18.73 (CH3), 127.70 (–HC=CH–), 140.58 (–HC=CH–), 146.21 (N=C), 177.95 (C=S). Analysis calculated for (II): C, 41.93; H, 6.33; N, 29.34.05, 22.39 S%. Found: C, 41.89; H, 6.25; N, 31.88%.

Refinement details  

Crystal data, data collection and structure refinement details are summarized in Table 3 ▸. Compounds (I) and (II) crystallized in the form of a very fine white powder. Since no single crystals of sufficient size and quality could be obtained, the crystal structures of both compounds were determined from X-ray powder diffraction patterns. The powder samples of (I) and (II) were lightly ground in a mortar, loaded into two Mylar foils and fixed onto the sample holder with a mask of suitable inter­nal diameter (8.0 mm). The powder X-ray diffraction data were collected at room temperature with a STOE transmission STADI-P diffractometer using monochromatic Cu Ka 1 radiation (λ= 1.54060 Å) selected with an incident beam curved-crystal germanium Ge(111) monochromator with a linear position-sensitive detector (PSD). The patterns were scanned over the angular range 5.0–80.0° (2θ). For pattern indexing, the extraction of the peak positions was carried out with the program WinPLOTR (Roisnel & Rodríguez-Carvajal, 2000 ▸). Pattern indexing was performed with the program DICVOL4.0 (Boultif & Louër, 2004 ▸). The first 20 lines of the powder pattern were indexed completely on the basis of a monoclinic cell for (I) and a triclinic cell for (II). The figures of merit (de Wolff et al., 1968 ▸; Smith & Snyder, 1979 ▸) are sufficiently acceptable to support the obtained indexing results [M(20) = 50.5, F(20) = 71.9 (0.0034, 83)] for (I) and [M(20) = 61.8, F(20) = 96.0 (0.0051, 41)] for (II). The best estimated space groups were P21/c in the monoclinic system for (I) and P Inline graphic in the triclinic system for (II).

Table 3. Experimental details.

  (I) (II)
Crystal data
Chemical formula C5H9N3O C5H9N3S
M r 127.15 143.21
Crystal system, space group Monoclinic, P21/c Triclinic, P Inline graphic
Temperature (K) 298 298
a, b, c () 11.1646(3), 5.13891(9), 13.0301(2) 5.86650(17), 8.0313(2), 9.0795(4)
, , () 90, 112.3496(11), 90 104.1407(18), 101.0403(19), 106.3511(17)
V (3) 691.43(3) 382.15(2)
Z 4 2
Radiation type Cu K 1, = 1.5406 Cu K 1, = 1.5406
(mm1) 0.74 3.11
Specimen shape, size (mm) Flat sheet, 8 8 Flat sheet, 8 8
 
Data collection
Diffractometer Stoe transmission Stadi-P Stoe transmission Stadi-P
Specimen mounting Powder loaded into two Mylar foils Powder loaded into two Mylar foils
Data collection mode Transmission Transmission
Scan method Step Step
2 values () 2min = 5 2max = 80 2step = 0.02 2min = 4.980 2max = 79.960 2step = 0.02
 
Refinement
R factors and goodness of fit R p = 0.027, R wp = 0.036, R exp = 0.029, R(F 2) = 0.02795, 2 = 1.613 R p = 0.033, R wp = 0.043, R exp = 0.034, R(F 2) = 0.02670, 2 = 1.664
No. of data points 3750 3750
No. of parameters 121 114
No. of restraints 0 1
H-atom treatment H-atom parameters not refined H-atom parameters not refined
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Computer programs: WinXPOW (Stoe Cie, 1999 ▸), EXPO2014 (Altomare et al., 2013 ▸), GSAS (Larson Von Dreele, 2004 ▸), ORTEP-3 for Windows (Farrugia, 2012 ▸), Mercury (Macrae et al., 2006 ▸) and publCIF (Westrip, 2010 ▸).

The whole powder diffraction patterns from 5 to 80° (2θ) for the two compounds (I) and (II) were subsequently refined with cell and resolution constraints (Le Bail et al., 1988 ▸) using the profile-matching option of the program FULLPROF (Rodríguez-Carvajal, 2001 ▸). The number of mol­ecules per unit cell was estimated to be Z = 4 for (I) and Z = 2 for (II). The initial crystal structures for (I) and (II) were determined by direct methods using the program EXPO2014 (Altomare et al., 2013 ▸). The models found by this program were introduced into the program GSAS (Larson & Von Dreele, 2004 ▸) implemented in EXPGUI (Toby, 2001 ▸) for Rietveld refinement. During the Rietveld refinements, the background was refined using a shifted Chebyshev polynomial with 20 coefficients. The effect of asymmetry of low-order peaks was corrected using a pseudo-Voigt description of the peak shape (Thompson et al., 1987 ▸), which allows for angle-dependent asymmetry with axial divergence (Finger et al., 1994 ▸) and microstrain broadening, as described by Stephens (1999 ▸). The two asymmetry parameters of this function, S/L and D/L, were both fixed at 0.022 during this refinement. Intensities were corrected from absorption effects with a function for a plate sample in transmission geometry with a μ·d value of 0.15 for (I) and 0.72 for (II) (μ is the absorption coefficient and d is the sample thickness). These μ·d values were determined experimentally.

Before the final refinement, all H atoms were introduced in geometrically calculated positions. The coordinates of these H atoms were refined with strict restraints on bond lengths and angles until a suitable geometry was obtained, after that they were fixed in the final stage of the refinement. No soft restraints were imposed for (I), while for (II) the CH3—CH bond was clearly stretched (close to 1.6 Å), therefore a single soft restraint was carried out to obtain a normal value (1.49 Å). The final refinement cycles were performed using isotropic atomic displacement parameters for the C, N and O atoms, an anisotropic atomic displacement parameter for S atom in (II) and a fixed global isotropic atomic displacement parameter for the H atoms. The preferred orientation was modelled with 12 coefficients using a spherical harmonics correction (Von Dreele, 1997 ▸) of intensities in the final refinement. The use of the preferred orientation correction leads to a better mol­ecular geometry with better agreement factors. The final Rietveld plots of the X-ray diffraction patterns for both (I) and (II) are given in Fig. 3 ▸.

Figure 3.

Figure 3

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The final Rietveld plots for (a) (I) and (b) (II). Experimental intensities are indicated by dots and the best-fit profile (upper trace) and difference pattern (lower trace) are shown as solid lines. The vertical bars indicate the calculated positions of the Bragg peaks.

Supplementary Material

Crystal structure: contains datablock(s) CROTON-CZ_Publ, I, II. DOI: 10.1107/S2056989015000663/cv5481sup1.cif

e-71-00168-sup1.cif (26.4KB, cif)

Rietveld powder data: contains datablock(s) I. DOI: 10.1107/S2056989015000663/cv5481Isup2.rtv

e-71-00168-Isup2.rtv (203.8KB, rtv)

Rietveld powder data: contains datablock(s) II. DOI: 10.1107/S2056989015000663/cv5481IIsup3.rtv

e-71-00168-IIsup3.rtv (204.8KB, rtv)

CCDC references: 1043290, 1043289

Additional supporting information: crystallographic information; 3D view; checkCIF report

Acknowledgments

The authors thank Professor I. Othman, Director General, and Professor Z. Ajji, Head of the Chemistry Department, for their support and encouragement during this work. We also thank Miss D. Naima for her kind assistance.

supplementary crystallographic information

Crystal data

C5H9N3S V = 382.15 (2) Å3
Mr = 143.21 Z = 2
Triclinic, P1 F(000) = 152
Hall symbol: -P 1 Dx = 1.245 Mg m−3
a = 5.86650 (17) Å Cu Kα1 radiation, λ = 1.5406 Å
b = 8.0313 (2) Å µ = 3.11 mm−1
c = 9.0795 (4) Å T = 298 K
α = 104.1407 (18)° Particle morphology: fine powder
β = 101.0403 (19)° white
γ = 106.3511 (17)° flat sheet, 8 × 8 mm
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Data collection

Stoe transmission Stadi-P diffractometer Data collection mode: transmission
Radiation source: sealed X-ray tube Scan method: step
Ge 111 monochromator 2θmin = 4.980°, 2θmax = 79.960°, 2θstep = 0.02°
Specimen mounting: Powder loaded into two Mylar foils
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Refinement

Least-squares matrix: full Profile function: CW Profile function number 4 with 21 terms Pseudovoigt profile coefficients as parameterized in (Thompson et al., 1987) Asymmetry correction of Finger et al., 1994. #1(GU) = 0.000 #2(GV) = 0.000 #3(GW) = 2.793 #4(GP) = 0.000 #5(LX) = 5.477 #6(ptec) = 2.45 #7(trns) = 0.00 #8(shft) = 0.0000 #9(sfec) = 0.00 #10(S/L) = 0.0220 #11(H/L) = 0.0220 #12(eta) = 0.6000 Peak tails are ignored where the intensity is below 0.0010 times the peak Aniso. broadening axis 0.0 0.0 1.0
Rp = 0.033 114 parameters
Rwp = 0.043 1 restraint
Rexp = 0.034 H-atom parameters not refined
R(F2) = 0.02670 (Δ/σ)max = 0.03
χ2 = 1.664 Background function: GSAS Background function number 1 with 20 terms. Shifted Chebyshev function of 1st kind 1: 590.360 2: -469.557 3: 198.126 4: -45.2586 5: -2.75624 6: 13.8508 7: 4.35563 8: -5.95029 9: -12.8815 10: 35.6051 11: -12.9276 12: -11.1488 13: 8.85293 14: -2.01034 15: -0.496121 16: 8.39616 17: -2.33367 18: -5.14527 19: 10.5079 20: -3.85249
3750 data points
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Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2)

x y z Uiso*/Ueq
C1 0.184 (2) 0.841 (2) 0.515 (2) 0.103 (6)*
H1A 0.15342 0.79934 0.39748 0.12*
H1B 0.2323 0.97016 0.55142 0.12*
H1C 0.02574 0.78525 0.53491 0.12*
C2 0.370 (2) 0.7688 (17) 0.5865 (18) 0.054 (5)*
H2 0.53963 0.83335 0.59455 0.055*
C3 0.325 (2) 0.6393 (16) 0.6524 (15) 0.034 (5)*
H3 0.14582 0.56255 0.63049 0.055*
C4 0.487 (3) 0.5747 (19) 0.7264 (19) 0.039 (5)*
H4 0.66632 0.65671 0.74816 0.055*
N1 0.4514 (17) 0.4461 (12) 0.7878 (15) 0.035 (4)*
N2 0.6486 (16) 0.4005 (12) 0.8462 (13) 0.021 (4)*
H1n2 0.79218 0.45838 0.841 0.05*
C5 0.611 (3) 0.2572 (16) 0.907 (2) 0.034 (4)*
N3 0.3681 (15) 0.1560 (12) 0.8849 (13) 0.017 (4)*
H1n3 0.34725 0.13246 0.97116 0.05*
H2n3 0.26401 0.20773 0.84645 0.05*
S1 0.8446 (6) 0.1980 (5) 0.9772 (6) 0.04081
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Atomic displacement parameters (Å2)

U11 U22 U33 U12 U13 U23
S1 0.032 (4) 0.039 (5) 0.082 (8) 0.026 (4) 0.043 (5) 0.035 (5)
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Geometric parameters (Å, º)

C1—H1A 0.999 C4—N1 1.274 (12)
C1—H1B 0.946 N1—N2 1.361 (10)
C1—H1C 0.983 N2—H1n2 0.856
C1—C2 1.49 (2) N2—C5 1.377 (13)
C2—H2 0.963 C5—N3 1.376 (13)
C2—C3 1.311 (13) C5—S1 1.638 (13)
C3—H3 1.008 N3—C5 1.376 (13)
C3—C4 1.352 (14) N3—H1n3 0.872
C4—H4 1.024 N3—H2n3 0.894
H1A—C1—H1B 109.0 C3—C4—N1 130.8 (16)
H1A—C1—H1C 106.2 H4—C4—N1 116.8
H1A—C1—C2 108.5 C4—N1—N2 118.6 (11)
H1B—C1—H1C 110.2 N1—N2—H1n2 119.6
H1B—C1—C2 113.8 N1—N2—C5 119.2 (10)
H1C—C1—C2 108.8 H1n2—N2—C5 121.2
C1—C2—H2 115.8 N2—C5—N3 115.6 (12)
C1—C2—C3 125.6 (13) N2—C5—S1 120.4 (11)
H2—C2—C3 118.2 N3—C5—S1 123.5 (9)
C2—C3—H3 116.8 C5—N3—H1n3 110.5
C2—C3—C4 128.4 (15) C5—N3—H2n3 112.2
H3—C3—C4 113.9 H1n3—N3—H2n3 113.2
C3—C4—H4 111.8
C4—N1—N2—C5 −177.4 (14) N1—N2—C5—N3 8.0 (19)
N2—N1—C4—C3 175.6 (15) C1—C2—C3—C4 −176.2 (15)
N1—N2—C5—S1 179.6 (11) C2—C3—C4—N1 −177.6 (16)
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Hydrogen-bond geometry (Å, º)

D—H···A D—H H···A D···A D—H···A
N3—H2N3···N1 0.89 2.17 2.641 (14) 112
N2—H1N2···S1i 0.86 2.83 3.473 (11) 133
N3—H1N3···S1ii 0.87 2.77 3.398 (11) 130
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Symmetry codes: (i) −x+2, −y+1, −z+2; (ii) −x+1, −y, −z+2.

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

Crystal structure: contains datablock(s) CROTON-CZ_Publ, I, II. DOI: 10.1107/S2056989015000663/cv5481sup1.cif

e-71-00168-sup1.cif (26.4KB, cif)

Rietveld powder data: contains datablock(s) I. DOI: 10.1107/S2056989015000663/cv5481Isup2.rtv

e-71-00168-Isup2.rtv (203.8KB, rtv)

Rietveld powder data: contains datablock(s) II. DOI: 10.1107/S2056989015000663/cv5481IIsup3.rtv

e-71-00168-IIsup3.rtv (204.8KB, rtv)

CCDC references: 1043290, 1043289

Additional supporting information: crystallographic information; 3D view; checkCIF report

Articles from Acta Crystallographica Section E: Crystallographic Communications are provided here courtesy of International Union of Crystallography

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