research communications
Crystal structures of crotonaldehyde semicarbazone and crotonaldehyde thiosemicarbazone from X-ray powder diffraction data
aDepartment of Chemistry, Atomic Energy Commission of Syria (AECS), PO Box 6091, Damascus, Syrian Arab Republic
*Correspondence e-mail: cscientific@aec.org.sy
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].
1. Chemical context
The chemistry of 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). 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.
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 (Beraldo2. Structural commentary
Compounds (I) and (II) crystallize in centrosymmetric space groups P21/c and P, respectively, with one molecule in the 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).
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3. 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. 2a). 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. 2b).
4. 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%.
5. details
Crystal data, data collection and structure . 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 Ka1 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 in the triclinic system for (II).
details are summarized in Table 3The 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 was estimated to be Z = 4 for (I) and Z = 2 for (II). The initial crystal structures for (I) and (II) were determined by 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 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 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 and d is the sample thickness). These μ·d values were determined experimentally.
Before the final , 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 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 was modelled with 12 coefficients using a spherical harmonics correction (Von Dreele, 1997) of intensities in the final The use of the 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.
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 No soft restraints were imposed for (I)Supporting information
10.1107/S2056989015000663/cv5481sup1.cif
contains datablocks CROTON-CZ_Publ, I, II. DOI:Rietveld powder data: contains datablock I. DOI: 10.1107/S2056989015000663/cv5481Isup2.rtv
Rietveld powder data: contains datablock II. DOI: 10.1107/S2056989015000663/cv5481IIsup3.rtv
The chemistry of
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). 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.Compounds (I) and (II) crystallize in centrosymmetric space groups P21/c and P1, respectively, with one molecule in the 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).
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. 2a). 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. 2b).
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%.
Crystal data, data collection and structure 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 P1 in the triclinic system for (II).
details are summarized in Table 2. 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 Ka1 radiation (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 was estimated to be Z = 4 for (I) and Z = 2 for (II). The initial crystal structures for (I) and (II) were determined by 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 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 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 and d is the sample thickness). These µ·d values were determined experimentally.
Before the final
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 No soft restraints were imposed for (I), while for (II) the bond CH3—CH was a clearly stretched (close to1.6 Å), therefore a single soft restraint was carried out to obtain a normal value (1.49 Å). The final 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 was modelled with 12 coefficients using a spherical harmonics correction (Von Dreele, 1997) of intensities in the final The use of the 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.For both compounds, data collection: WinXPOW (Stoe & Cie, 1999). Data reduction: WinXPOW (Stoe & Cie, 1999) for (I). For both compounds, program(s) used to solve structure: EXPO2014 (Altomare et al., 2013); program(s) used to refine structure: GSAS (Larson & Von Dreele, 2004); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012), Mercury (Macrae et al., 2006); software used to prepare material for publication: publCIF (Westrip, 2010).
Fig. 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. | |
Fig. 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. | |
Fig. 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. |
C5H9N3O | Z = 4 |
Mr = 127.15 | F(000) = 272 |
Monoclinic, P21/c | Dx = 1.222 Mg m−3 |
Hall symbol: -P 2ybc | Cu Kα1 radiation, λ = 1.5406 Å |
a = 11.1646 (3) Å | µ = 0.74 mm−1 |
b = 5.13891 (9) Å | T = 298 K |
c = 13.0301 (2) Å | Particle morphology: fine powder |
β = 112.3496 (11)° | white |
V = 691.43 (3) Å3 | 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 = 5°, 2θmax = 80°, 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. Microstrain broadening by P.W. Stephens, (1999. #1(GU) = 0.000 #2(GV) = 0.000 #3(GW) = 10.054 #4(GP) = 0.000 #5(LX) = 2.972 #6(ptec) = 0.00 #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 #13(S400 ) = 2.1E-01 #14(S040 ) = 3.3E-01 #15(S004 ) = 4.2E-02 #16(S220 ) = 2.1E-02 #17(S202 ) = 4.8E-03 #18(S022 ) = 8.7E-02 #19(S301 ) = -3.5E-03 #20(S103 ) = 5.2E-02 #21(S121 ) = 5.4E-02 Peak tails are ignored where the intensity is below 0.0010 times the peak Aniso. broadening axis 0.0 0.0 1.0 |
Rp = 0.027 | 121 parameters |
Rwp = 0.036 | 0 restraints |
Rexp = 0.029 | H-atom parameters not refined |
R(F2) = 0.02795 | Weighting scheme based on measured s.u.'s |
χ2 = 1.613 | (Δ/σ)max = 0.03 |
3750 data points | Background function: GSAS Background function number 1 with 20 terms. Shifted Chebyshev function of 1st kind 1: 983.478 2: -916.772 3: 421.914 4: -92.3775 5: -9.18321 6: 30.2365 7: -2.25826 8: -10.7421 9: -19.9256 10: 25.6982 11: -24.5216 12: 4.20376 13: 6.93721 14: -3.88406 15: -7.36711 16: 7.71847 17: -1.82508 18: -0.259371 19: -0.220296 20: 0.765767 |
C5H9N3O | V = 691.43 (3) Å3 |
Mr = 127.15 | Z = 4 |
Monoclinic, P21/c | Cu Kα1 radiation, λ = 1.5406 Å |
a = 11.1646 (3) Å | µ = 0.74 mm−1 |
b = 5.13891 (9) Å | T = 298 K |
c = 13.0301 (2) Å | flat sheet, 8 × 8 mm |
β = 112.3496 (11)° |
Stoe transmission Stadi-P diffractometer | Scan method: step |
Specimen mounting: Powder loaded into two Mylar foils | 2θmin = 5°, 2θmax = 80°, 2θstep = 0.02° |
Data collection mode: transmission |
Rp = 0.027 | 3750 data points |
Rwp = 0.036 | 121 parameters |
Rexp = 0.029 | 0 restraints |
R(F2) = 0.02795 | H-atom parameters not refined |
χ2 = 1.613 |
x | y | z | Uiso*/Ueq | ||
C1 | 0.935 (2) | 0.8319 (18) | 0.3282 (11) | 0.057 (5)* | |
H1a | 0.88432 | 0.92372 | 0.25964 | 0.075* | |
H1b | 0.96701 | 0.95714 | 0.38819 | 0.075* | |
H1c | 1.00844 | 0.74948 | 0.31821 | 0.075* | |
C2 | 0.855 (2) | 0.6310 (16) | 0.3552 (13) | 0.052 (4)* | |
H2 | 0.8297 | 0.48475 | 0.30627 | 0.075* | |
C3 | 0.8056 (15) | 0.6448 (14) | 0.4352 (9) | 0.033 (4)* | |
H3 | 0.80211 | 0.8092 | 0.46492 | 0.05* | |
C4 | 0.7367 (18) | 0.4405 (17) | 0.4558 (11) | 0.032 (4)* | |
H4 | 0.73987 | 0.27746 | 0.42622 | 0.075* | |
N1 | 0.7027 (14) | 0.4632 (13) | 0.5417 (7) | 0.025 (3)* | |
N2 | 0.6313 (12) | 0.2520 (15) | 0.5530 (7) | 0.031 (3)* | |
H1n2 | 0.60928 | 0.12885 | 0.50191 | 0.05* | |
C5 | 0.5708 (15) | 0.252 (2) | 0.6285 (11) | 0.029 (4)* | |
O1 | 0.5060 (12) | 0.0728 (12) | 0.6388 (6) | 0.029 (3)* | |
N3 | 0.6041 (15) | 0.4651 (13) | 0.6956 (9) | 0.024 (3)* | |
H1n3 | 0.55477 | 0.51321 | 0.73425 | 0.05* | |
H2n3 | 0.67532 | 0.55182 | 0.70648 | 0.05* |
C1—C2 | 1.493 (17) | C4—H4 | 0.928 |
C1—H1a | 0.978 | N1—N2 | 1.387 (11) |
C1—H1b | 0.970 | N2—H1n2 | 0.883 |
C1—H1c | 0.975 | N2—C5 | 1.390 (10) |
C2—C3 | 1.353 (11) | C5—O1 | 1.210 (11) |
C2—H2 | 0.956 | C5—N3 | 1.361 (11) |
C3—C4 | 1.387 (13) | N3—H1n3 | 0.911 |
C3—H3 | 0.936 | N3—H2n3 | 0.875 |
C4—N1 | 1.317 (11) | ||
H1a—C1—H1b | 108.9 | C3—C4—N1 | 117.2 (12) |
H1a—C1—H1c | 108.1 | H4—C4—N1 | 120.1 |
H1a—C1—C2 | 111.0 | C4—N1—N2 | 112.5 (9) |
H1b—C1—H1c | 109.0 | N1—N2—H1n2 | 119.2 |
H1b—C1—C2 | 109.9 | N1—N2—C5 | 121.9 (9) |
H1c—C1—C2 | 109.9 | H1n2—N2—C5 | 117.6 |
C1—C2—H2 | 115.9 | N2—C5—O1 | 123.3 (11) |
C1—C2—C3 | 126.9 (9) | N2—C5—N3 | 111.6 (11) |
H2—C2—C3 | 116.9 | O1—C5—N3 | 124.8 (11) |
C2—C3—H3 | 117.3 | C5—N3—H1n3 | 119.9 |
C2—C3—C4 | 121.8 (10) | C5—N3—H2n3 | 121.6 |
H3—C3—C4 | 119.4 | H1n3—N3—H2n3 | 118.4 |
C3—C4—H4 | 119.5 | ||
C4—N1—N2—C5 | −171.0 (13) | N1—N2—C5—N3 | −7.4 (18) |
N2—N1—C4—C3 | 178.3 (13) | C1—C2—C3—C4 | −177.3 (16) |
N1—N2—C5—O1 | 178.6 (13) | C2—C3—C4—N1 | 174.0 (15) |
D—H···A | D—H | H···A | D···A | D—H···A |
N3—H2N3···N1 | 0.87 | 2.33 | 2.629 (19) | 100 |
N2—H1N2···O1i | 0.88 | 2.07 | 2.910 (11) | 158 |
N3—H1N3···O1ii | 0.91 | 2.04 | 2.914 (18) | 162 |
Symmetry codes: (i) −x+1, −y, −z+1; (ii) −x+1, y+1/2, −z+3/2. |
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 |
C5H9N3S | γ = 106.3511 (17)° |
Mr = 143.21 | V = 382.15 (2) Å3 |
Triclinic, P1 | Z = 2 |
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)° | flat sheet, 8 × 8 mm |
β = 101.0403 (19)° |
Stoe transmission Stadi-P diffractometer | Scan method: step |
Specimen mounting: Powder loaded into two Mylar foils | 2θmin = 4.980°, 2θmax = 79.960°, 2θstep = 0.02° |
Data collection mode: transmission |
Rp = 0.033 | 3750 data points |
Rwp = 0.043 | 114 parameters |
Rexp = 0.034 | 1 restraint |
R(F2) = 0.02670 | H-atom parameters not refined |
χ2 = 1.664 |
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 |
Symmetry codes: (i) −x+2, −y+1, −z+2; (ii) −x+1, −y, −z+2. |
D—H···A | D—H | H···A | D···A | D—H···A |
N3—H2N3···N1 | 0.87 | 2.33 | 2.629 (19) | 100 |
N2—H1N2···O1i | 0.88 | 2.07 | 2.910 (11) | 158 |
N3—H1N3···O1ii | 0.91 | 2.04 | 2.914 (18) | 162 |
Symmetry codes: (i) −x+1, −y, −z+1; (ii) −x+1, y+1/2, −z+3/2. |
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 |
Symmetry codes: (i) −x+2, −y+1, −z+2; (ii) −x+1, −y, −z+2. |
Experimental details
(I) | (II) | |
Crystal data | ||
Chemical formula | C5H9N3O | C5H9N3S |
Mr | 127.15 | 143.21 |
Crystal system, space group | Monoclinic, P21/c | Triclinic, P1 |
Temperature (K) | 298 | 298 |
a, b, c (Å) | 11.1646 (3), 5.13891 (9), 13.0301 (2) | 5.86650 (17), 8.0313 (2), 9.0795 (4) |
α, β, γ (°) | 90, 112.3496 (11), 90 | 104.1407 (18), 101.0403 (19), 106.3511 (17) |
V (Å3) | 691.43 (3) | 382.15 (2) |
Z | 4 | 2 |
Radiation type | Cu Kα1, λ = 1.5406 Å | Cu Kα1, λ = 1.5406 Å |
µ (mm−1) | 0.74 | 3.11 |
Specimen shape, size (mm) | Flat sheet, 8 × 8 | Flat sheet, 8 × 8 |
Data collection | ||
Diffractometer | Stoe transmission Stadi-P diffractometer | Stoe transmission Stadi-P diffractometer |
Specimen mounting | Powder loaded into two Mylar foils | Powder loaded into two Mylar foils |
Data collection mode | Transmission | Transmission |
Scan method | Step | Step |
2θ values (°) | 2θmin = 5 2θmax = 80 2θstep = 0.02 | 2θmin = 4.980 2θmax = 79.960 2θstep = 0.02 |
Refinement | ||
R factors and goodness of fit | Rp = 0.027, Rwp = 0.036, Rexp = 0.029, R(F2) = 0.02795, χ2 = 1.613 | Rp = 0.033, Rwp = 0.043, Rexp = 0.034, R(F2) = 0.02670, χ2 = 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), publCIF (Westrip, 2010).
Acknowledgements
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.
References
Alomar, K., Gaumet, V., Allain, M., Bouet, G. & Landreau, A. (2012). J. Inorg. Biochem. 115, 36–43. Google Scholar
Altomare, A., Cuocci, C., Giacovazzo, C., Moliterni, A., Rizzi, R., Corriero, N. & Falcicchio, A. (2013). J. Appl. Cryst. 46, 1231–1235. Web of Science CrossRef CAS IUCr Journals Google Scholar
Beraldo, H. & Gambinob, D. (2004). Mini Rev. Med. Chem. 4, 31–39. PubMed CAS Google Scholar
Beraldo, H., Sinisterra, R. D., Teixeira, L. R., Vieira, R. P. & Doretto, M. C. (2002). Biochem. Biophys. Res. Commun. 296, 241–246. Web of Science CrossRef PubMed CAS Google Scholar
Boultif, A. & Louër, D. (2004). J. Appl. Cryst. 37, 724–731. Web of Science CrossRef CAS IUCr Journals Google Scholar
Carballo, R., Pino-Cuevas, A. & Vázquez-López, E. M. (2014). Acta Cryst. E70, o970. Google Scholar
Casas, J. S., Garc\?ía-Tasende, M. S. & Sordo, J. (2000). Coord. Chem. Rev. 209, 197–261. Google Scholar
Farrugia, L. J. (2012). J. Appl. Cryst. 45, 849–854. Web of Science CrossRef CAS IUCr Journals Google Scholar
Finger, L. W., Cox, D. E. & Jephcoat, A. P. (1994). J. Appl. Cryst. 27, 892–900. CrossRef CAS Web of Science IUCr Journals Google Scholar
Gan, C., Cui, J., Su, S., Lin, Q., Jia, L., Fan, L. & Huang, Y. (2014). Steroids, 87, 99–107. Google Scholar
Garg, B. S. & Jain, V. K. (1988). Microchem. J. 38, 144–169. CrossRef CAS Google Scholar
Greenbaum, D. C., Mackey, Z., Hansell, E., Doyle, P. S., Gut, J., Caffrey, C. R., Lehrman, J., Rosenthal, P. J., McKerrow, J. H. & Chibale, K. (2004). J. Med. Chem. 47, 3212–3219. Google Scholar
Kasuga, N. C., Sekino, K., Ishikawa, M., Honda, A., Yokoyama, M., Nakano, S., Shimada, N., Koumo, C. & Nomiya, K. (2003). J. Inorg. Biochem. 96, 298–310. Web of Science CSD CrossRef PubMed CAS Google Scholar
Küçükgüzel, G., Kocatepe, A., De Clercq, E., Şahin, F. & Güllüce, M. (2006). Eur. J. Med. Chem. 41, 353–359. Google Scholar
Larson, A. C. & Von Dreele, R. B. (2004). GSAS. Report LAUR 86-748. Los Alamos National Laboratory, New Mexico, USA. Google Scholar
Le Bail, A., Duroy, H. & Fourquet, J. L. (1988). Mater. Res. Bull. 23, 447–452. CrossRef CAS Web of Science Google Scholar
Macrae, C. F., Edgington, P. R., McCabe, P., Pidcock, E., Shields, G. P., Taylor, R., Towler, M. & van de Streek, J. (2006). J. Appl. Cryst. 39, 453–457. Web of Science CrossRef CAS IUCr Journals Google Scholar
Mikhaleva, A. I., Ivanov, A. V., Vasil'tsov, A. M., Ushakov, I. A., Ma, J. S. & Yang, G. (2008). Chem. Heterocycl. Compd, 44, 1117–1122. Google Scholar
Naik, D. V. & Palenik, G. J. (1974). Acta Cryst. B30, 2396–2401. CSD CrossRef IUCr Journals Web of Science Google Scholar
Oliveira, R. B. de, de Souza-Fagundes, E. M., Soares, R. P. P., Andrade, A. A., Krettli, A. U. & Zani, C. L. (2008). Eur. J. Med. Chem. 43, 1983–1988. Google Scholar
Pelosi, G., Pelizzi, C., Belicchi Ferrari, M., Rodríguez-Argüelles, M. C., Vieito, C. & Sanmartín, J. (2005). Acta Cryst. C61, o589–o592. Web of Science CSD CrossRef CAS IUCr Journals Google Scholar
Reddy, M. S., Sarala, Y., Jagadeesh, M., Das, S. K. & Ammireddy, V. R. (2014). Acta Cryst. E70, o846. Google Scholar
Rodríguez-Carvajal, J. (2001). Commission on Powder Diffraction (IUCr) Newsletter, 26, 12–19. Google Scholar
Roisnel, T. & Rodríguez-Carvajal, J. (2000). Mater. Sci. Forum, 378–381, 118–123. Google Scholar
Sarojini, B. K., Narayana, B., Bindya, S., Yathirajan, H. S. & Bolte, M. (2007). Acta Cryst. E63, o2946. Web of Science CSD CrossRef IUCr Journals Google Scholar
Smith, G. S. & Snyder, R. L. (1979). J. Appl. Cryst. 12, 60–65. CrossRef CAS IUCr Journals Web of Science Google Scholar
Stephens, P. W. (1999). J. Appl. Cryst. 32, 281–289. Web of Science CrossRef CAS IUCr Journals Google Scholar
Stoe & Cie (1999). WinXPOW. Stoe & Cie, Darmstadt, Germany. Google Scholar
Teixeira, L. R., Sinisterra, R. D., Vieira, R. P., Doretto, M. C. & Beraldo, H. (2003). J. Incl. Phenom. Macrocycl. Chem. 47, 77–82. Google Scholar
Thompson, P., Cox, D. E. & Hastings, J. B. (1987). J. Appl. Cryst. 20, 79–83. CrossRef CAS Web of Science IUCr Journals Google Scholar
Toby, B. H. (2001). J. Appl. Cryst. 34, 210–213. Web of Science CrossRef CAS IUCr Journals Google Scholar
Von Dreele, R. B. (1997). J. Appl. Cryst. 30, 517–525. CrossRef CAS Web of Science IUCr Journals Google Scholar
Wang, J.-L., Jia, Y.-J. & Yu, M. (2004). Acta Cryst. E60, o662–o663. Web of Science CSD CrossRef IUCr Journals Google Scholar
Westrip, S. P. (2010). J. Appl. Cryst. 43, 920–925. Web of Science CrossRef CAS IUCr Journals Google Scholar
Wolff, P. M. de (1968). J. Appl. Cryst. 1, 108–113. CrossRef IUCr Journals Web of Science Google Scholar
Yathirajan, H. S., Bindya, S., Narayana, B., Sarojini, B. K. & Bolte, M. (2006). Acta Cryst. E62, o5925–o5926. Web of Science CSD CrossRef IUCr Journals Google Scholar
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