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

Crotonaldehyde semicarbazone {systematic name: (E)-2-[(E)-but-2-en-1-yl-idene]hydrazinecarboxamide}, C5H9N3O, (I), and crotonaldehyde thio-semi-carba-zone {systematic name: (E)-2-[(E)-but-2-en-1-yldene]hydra-zinecarbo--thio-amide}, 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 hydro-chloride and thio-semicarbazide, respectively. Each mol-ecule has an intra-molecular 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 thio-semicarbazide mean plane) is 9.12 (5)°. The crystal packing is different in the two compounds: in (I) inter-molecular N-H⋯O hydrogen bonds link the mol-ecules into layers parallel to the bc plane, while weak inter-molecular N-H⋯S hydrogen bonds in (II) link the mol-ecules 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.

Structural commentary

Compounds (I) and (II) crystallize in centrosymmetric space groups P2 and P , 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

Symmetry codes: (i) ; (ii) .

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

Symmetry codes: (i) ; (ii) .

Figure 1

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-n class="Species">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 R 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

(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 K 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 P2 in the monoclinic system for (I) and P 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
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

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

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.

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

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

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

CCDC references: 1043290, 1043289

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

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

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

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

	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

	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)

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)

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