Crystal structures of the Schiff base derivatives (E)-N′-[(1H-indol-3-yl)methyl­idene]isonicotino­hydrazide ethanol monosolvate and (E)-N-methyl-2-[1-(2-oxo-2H-chromen-3-yl)ethyl­idene]hydrazinecarbo­thio­amide

Saranya, S.; Haribabu, J.; Bhuvanesh, N.S.P.; Karvembu, R.; Gayathri, D.

doi:10.1107/S205698901700411X

research communications

CRYSTALLOGRAPHIC
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ISSN: 2056-9890

Volume 73| Part 4| April 2017| Pages 594-597

https://doi.org/10.1107/S205698901700411X

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Crystal structures of the Schiff base derivatives (E)-N′-[(1H-indol-3-yl)methylidene]isonicotinohydrazide ethanol monosolvate and (E)-N-methyl-2-[1-(2-oxo-2H-chromen-3-yl)ethylidene]hydrazinecarbothioamide

Sivaraj Saranya,^a Jebiti Haribabu,^b Nattamai S. P. Bhuvanesh,^c Ramasamy Karvembu ^b and Dasararaju Gayathri ^d ^*

^aDepartment of Biotechnology, Dr. M.G.R. Educational and Research Institute University, Maduravoyal, Chennai 600 095, India, ^bDepartment of Chemistry, National Institute of Technology, Tiruchirappalli 620 015, India, ^cDepartment of Chemistry, Texas A & M University, College Station, TX 77842, USA, and ^dCentre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025, India
^*Correspondence e-mail: drdgayathri@gmail.com

Edited by H. Ishida, Okayama University, Japan (Received 18 December 2016; accepted 14 March 2017; online 24 March 2017)

The crystal structures of two title Schiff base derivatives, C₁₅H₁₂N₄O·C₂H₆O (1·EtOH) and C₁₃H₁₃N₃O₂S (2), were determined at 110 and 100 K, respectively. In the crystal of compound 1·EtOH, the (E)-N′-[(1H-indol-3-yl)methylidene]isonicotinohydrazide and ethanol molecules are linked by O—H⋯O, N—H⋯O and N—H⋯N hydrogen bonds, forming a tape structure running along the b-axis direction. The tapes are weakly linked via a C—H⋯N interaction. In the crystal of compound 2, (E)-N-methyl-2-[1-(2-oxo-2H-chromen-3-yl)ethylidene]hydrazinecarbothioamide molecules are linked via N—H⋯O and C—H⋯O hydrogen bonds, forming a helical chain along the b-axis direction. The chains are further linked into a layer expanding parallel to (102) through C—H⋯S interactions.

Keywords: crystal structure; Schiff base derivatives; isonicotinohydrazide; hydrazinecarbothioamide.

CCDC references: 1537754; 1537753

1. Chemical context

Schiff base derivatives are a biologically versatile class of compounds possessing diverse activities, such as anti-oxidant (Haribabu, Subhashree et al., 2015 , 2016 ), anti-inflammatory (Alam et al., 2012 ), anti-cancer (Creaven et al., 2010 ; Haribabu, Jeyalakshmi et al., 2015 , 2016 ), anti-bacterial (Sondhi et al., 2006 ), anti-fungal (Jarrahpour et al., 2007 ), anti-convulsant (Bhat & Al-Omar, 2011 ). Schiff bases have gained special attention in pharmacophore research and in the development of several bioactive lead molecules. They are widely used as catalysts, corrosion inhibitors and intermediates in organic synthesis, and also play a potential role in the development of coordination chemistry (Muralisankar et al., 2016 ). As part of our studies in this area, we have synthesized the title Schiff base compounds, 1·EtOH and 2, and determined their crystal structures.

2. Structural commentary

The molecular structures ((Figs. 1 and 2) of both 1 and 2 are non-planar, as evidenced by the torsion angles N3—C10—C11—C12 [42.5 (3)°] in 1 and C1—C2—C10—N1 [−152.0 (2)°] in 2. The mean plane of the central chain C9/N2/N3/C10/O1 in 1 makes dihedral angles of 6.91 (12) and 42.71 (13)°, respectively, with the C1–C8/N1 ring system and the pyridine C11–C15/N4 ring. In molecule 2, the dihedral angle between the C1–C9/O1 ring system and the mean plane of the C10/N1/N2/C12/N3/C13 chain is 30.36 (9)°.

Figure 1
The molecular structure of compound 1·EtOH, with the atom labelling. Displacement ellipsoids of non-H atoms are drawn at 30% probability level.

Figure 2
The molecular structure of compound 2, with the atom labelling. Displacement ellipsoids of non-H atoms are drawn at 30% probability level.

3. Supramolecular features

The crystal packing of 1·EtOH features O—H⋯O, N—H⋯O and N—H⋯N hydrogen bonds (Table 1), which link the molecules into a tape structure running along the b-axis direction (Fig. 3). The tapes are weakly linked via a C—H⋯N interaction (Table 1). In the N—H⋯O and N—H⋯N hydrogen bonds, atoms N1 and N3 act as donors to atoms O1 and N4, respectively, generating C(9) and C(7) chain motifs. The C—H⋯N interaction generates a C(8) chain. Atom O1S of the ethanol molecule acts as a donor in forming the O—H⋯O hydrogen bond with atom O1, which acts as a double acceptor.

Table 1
Hydrogen-bond geometry (Å, °) for 1·EtOH

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1⋯O1ⁱ	0.88	2.05	2.871 (3)	156
N3—H3⋯N4ⁱⁱ	0.88	2.14	2.979 (3)	159
C5—H5⋯N2ⁱⁱⁱ	0.95	2.62	3.236 (3)	123
O1S—H1S⋯O1	0.84	1.90	2.742 (3)	177
Symmetry codes: (i) x, y-1, z; (ii) $[-x, y-{\script{1\over 2}}, -z+{\script{3\over 2}}]$ ; (iii) $[x+{\script{1\over 2}}, -y+{\script{1\over 2}}, -z+1]$ .

Figure 3
A packing diagram of compound 1·EtOH, viewed along the a axis, showing the O—H⋯O, N—H⋯O, N—H⋯N and C—H⋯N interactions (dashed lines). For clarity, H atoms not involved in these interactions have been omitted.

In 2, the crystal packing features N—H⋯O, C—H⋯O and C—H⋯S interactions (Table 2). The molecules are linked via N—H⋯O and C—H⋯O hydrogen bonds, forming a helical chain along the b-axis direction (Fig. 4). The chains are further linked via C—H⋯S interactions, forming a layer expanding parallel to (102). Atoms N2 and C11 act as donors to the double acceptor O2, generating C(7) and C(6) chains, respectively. As a result of these two hydrogen bonds, an R₂¹(7) ring motif is generated. In the C—H⋯S interactions, atoms C7 and C11 act as donors to the double acceptor S1, generating C(11) and C(7) chains, respectively.

Table 2
Hydrogen-bond geometry (Å, °) for 2

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N2—H2⋯O2ⁱ	0.88	2.39	3.269 (3)	175
C11—H11A⋯O2ⁱ	0.98	2.47	3.109 (3)	123
C7—H7⋯S1ⁱⁱ	0.95	2.85	3.711 (3)	151
C11—H11B⋯S1ⁱⁱⁱ	0.98	2.87	3.728 (3)	146
Symmetry codes: (i) $[-x+1, y+{\script{1\over 2}}, -z+{\script{1\over 2}}]$ ; (ii) $[x-1, -y+{\script{3\over 2}}, z+{\script{1\over 2}}]$ ; (iii) $[-x+1, y-{\script{1\over 2}}, -z+{\script{1\over 2}}]$ .

Figure 4
A crystal packing view of 2 along the a axis, showing the intermolecular hydrogen-bonded network formed by N—H⋯O, C—H⋯O and C—H⋯S interactions (dashed lines). For clarity, H atoms not involved in these interactions have been omitted.

4. Database survey

A search of the Cambridge Structural Database (Groom et al., 2016 ) for the substructures 1 and 2 revealed several related Schiff base derivatives, including those with refcodes ADEKAW, ACIPIN, ADEZAL02 and APAQEP reported by Qiu et al. (2006 ), Lobana et al. (2012 ), Ilies et al. (2013 ) and Chainok et al. (2016 ), respectively.

5. Synthesis and crystallization

Compound 1 was synthesized by condensing equimolar amounts of 1H-indole-3-carbaldehyde (145 mg, 1 mmol) with nicotinic acid hydrazide (137 mg, 1 mmol) in ethanol. The reaction mixture was then refluxed on a water bath for 5 h and poured into crushed ice. The corresponding solid Schiff base that formed was filtered, washed several times with distilled water and dried under vacuum. The compound was recrystallized from an ethanol–chloroform (1:3) solvent mixture, yielding the ethanol solvate compound, 1·EtOH. Similarly, compound 2 was synthesized from equimolar amounts of 3-acetyl-2H-chromen-2-one (188 mg, 1 mmol) with N-methylhydrazinecarbothioamide (105 mg, 1 mmol) in ethanol. Compound 2 was also recrystallized from an ethanol–chloroform (1:3) solvent mixture.

6. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 3. H atoms were refined as riding with N—H = 0.88, C—H = 0.95 or 0.98 Å and U_iso(H) = 1.2 or 1.5U_eq(parent atom). For 1·EtOH, the methylene H atoms of the ethanol solvent molecule were refined independently under strong bond-length and angle restraints using DFIX to avoid a large residual electron-density peak near the methylene C atom caused by the usual riding treatment of the H atoms. In 2, TWINABS was employed to correct the data for absorption effects, as well as to separate hkl files for the domains with major and minor components; the twin ratio was observed to be 91:9. In the refinement, only the data of the major domain were used.

Table 3
Experimental details

	1·EtOH	2
Crystal data
Chemical formula	C₁₅H₁₂N₄O·C₂H₆O	C₁₃H₁₃N₃O₂S
M_r	310.35	275.32
Crystal system, space group	Orthorhombic, P2₁2₁2₁	Monoclinic, P2₁/c
Temperature (K)	110	100
a, b, c (Å)	9.4692 (18), 9.9821 (19), 16.682 (3)	9.289 (4), 9.616 (4), 14.474 (6)
α, β, γ (°)	90, 90, 90	90, 90.825 (4), 90
V (Å³)	1576.9 (5)	1292.8 (9)
Z	4	4
Radiation type	Mo Kα	Mo Kα
μ (mm⁻¹)	0.09	0.25
Crystal size (mm)	0.50 × 0.37 × 0.13	0.49 × 0.46 × 0.31

Data collection
Diffractometer	Bruker APEXII CCD	Bruker APEXII CCD
Absorption correction	Multi-scan (SADABS; Bruker, 2008 )	Multi-scan (TWINABS; Bruker, 2012 )
T_min, T_max	0.618, 0.681	0.534, 0.746
No. of measured, independent and observed [I > 2σ(I)] reflections	39878, 3616, 3527	5480, 2902, 2285
R_int	0.054	0.044
(sin θ/λ)_max (Å⁻¹)	0.651	0.651

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.043, 0.119, 0.98	0.048, 0.116, 1.10
No. of reflections	3616	2902
No. of parameters	216	174
No. of restraints	3	0
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	1.50, −0.36	0.30, −0.35
Absolute structure	Flack x determined using 1491 quotients [(I⁺)−(I⁻)]/[(I⁺)+(I⁻)] (Parsons et al., 2013 )	–
Absolute structure parameter	−0.2 (3)	–
Computer programs: APEX2 and SAINT (Bruker, 2013), SHELXS2014 and SHELXS2013 (Sheldrick, 2008 ), SHELXL2013 and SHELXL2016 (Sheldrick, 2015 ) and PLATON (Spek, 2015 ).

Supporting information

CCDC references: 1537754; 1537753

Crystal structure: contains datablocks Global, 2, 1.EtOH. DOI: https://doi.org/10.1107/S205698901700411X/is5471sup1.cif

Structure factors: contains datablock 1.EtOH. DOI: https://doi.org/10.1107/S205698901700411X/is54711.EtOHsup4.hkl

Structure factors: contains datablock 2. DOI: https://doi.org/10.1107/S205698901700411X/is54712sup5.hkl

Supporting information file. DOI: https://doi.org/10.1107/S205698901700411X/is54711.EtOHsup4.cml

Supporting information file. DOI: https://doi.org/10.1107/S205698901700411X/is54712sup5.cml

checkCIF report

Computing details top

For both compounds, data collection: APEX2 (Bruker, 2013); cell refinement: SAINT (Bruker, 2013); data reduction: SAINT (Bruker, 2013). Program(s) used to solve structure: SHELXS2014 (Sheldrick, 2008) for 1.EtOH; SHELXS2013 (Sheldrick, 2008) for (2). Program(s) used to refine structure: SHELXL2016 (Sheldrick, 2015) for 1.EtOH; SHELXL2013 (Sheldrick, 2008) for (2). For both compounds, molecular graphics: PLATON (Spek, 2015). Software used to prepare material for publication: SHELXL2016 (Sheldrick, 2015) and PLATON (Spek, 2015) for 1.EtOH; SHELXL2013 (Sheldrick, 2015) and PLATON (Spek, 2015) for (2).

(1.EtOH) (E)-N'-[(1H-Indol-3-yl)methylidene]isonicotinohydrazide ethanol monosolvate top

Crystal data top

C₁₅H₁₂N₄O·C₂H₆O	D_x = 1.307 Mg m⁻³
M_r = 310.35	Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, P2₁2₁2₁	Cell parameters from 9846 reflections
a = 9.4692 (18) Å	θ = 2.4–27.5°
b = 9.9821 (19) Å	µ = 0.09 mm⁻¹
c = 16.682 (3) Å	T = 110 K
V = 1576.9 (5) Å³	Block, colorless
Z = 4	0.50 × 0.37 × 0.13 mm
F(000) = 656

Data collection top

Bruker APEXII CCD diffractometer	3527 reflections with I > 2σ(I)
φ and ω scans	R_int = 0.054
Absorption correction: multi-scan (SADABS; Bruker, 2008)	θ_max = 27.6°, θ_min = 2.4°
T_min = 0.618, T_max = 0.681	h = −12→12
39878 measured reflections	k = −12→12
3616 independent reflections	l = −21→21

Refinement top

Refinement on F²	Hydrogen site location: mixed
Least-squares matrix: full	H atoms treated by a mixture of independent and constrained refinement
R[F² > 2σ(F²)] = 0.043	w = 1/[σ²(F_o²) + (0.077P)² + 0.9574P] where P = (F_o² + 2F_c²)/3
wR(F²) = 0.119	(Δ/σ)_max = 0.004
S = 0.98	Δρ_max = 1.50 e Å⁻³
3616 reflections	Δρ_min = −0.36 e Å⁻³
216 parameters	Absolute structure: Flack x determined using 1491 quotients [(I⁺)-(I^-)]/[(I⁺)+(I^-)] (Parsons et al., 2013)
3 restraints	Absolute structure parameter: −0.2 (3)

Special details top

Experimental. SADABS-2014/3 (Bruker, 2014) was used for absorption correction. wR2(int) was 0.1205 before and 0.0824 after correction. The Ratio of minimum to maximum transmission is 0.9082. The λ/2 correction factor is not present.

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. 1. Fixed Uiso; at 1.2 times of: all C(H) groups, all N(H) groups and at 1.5 times of: C2S(H2SA, H2SB, H2SC) and O(H) groups 2. a. Aromatic/amide H refined with riding coordinates: N1(H1), N3(H3), C3(H3A), C4(H4), C5(H5), C6(H6), C7(H7), C9(H9), C12(H12), C13(H13), C14(H14), C15(H15) b. Idealised Me refined as rotating group: C11(H11A, H11B, H11C) 3. Strong restraints with DFIX were employed for methylene hydrogen atoms of the ethanol solvent molecule.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
O1	0.41425 (19)	0.67417 (16)	0.63518 (11)	0.0184 (4)
N1	0.4971 (2)	−0.05011 (19)	0.64904 (12)	0.0157 (4)
H1	0.492857	−0.137698	0.654508	0.019*
N2	0.3980 (2)	0.40446 (18)	0.66721 (11)	0.0140 (4)
N3	0.2999 (2)	0.49844 (19)	0.69437 (12)	0.0137 (4)
H3	0.228694	0.472947	0.724635	0.016*
N4	−0.0322 (2)	0.8812 (2)	0.74337 (13)	0.0195 (4)
C1	0.5943 (2)	0.0185 (2)	0.60295 (13)	0.0143 (4)
C2	0.5644 (2)	0.1570 (2)	0.60882 (13)	0.0135 (4)
C3	0.6449 (3)	0.2483 (2)	0.56436 (14)	0.0166 (5)
H3A	0.625228	0.341561	0.566138	0.020*
C4	0.7543 (3)	0.1987 (3)	0.51768 (15)	0.0201 (5)
H4	0.809673	0.259218	0.486964	0.024*
C5	0.7852 (3)	0.0605 (3)	0.51472 (15)	0.0204 (5)
H5	0.862792	0.030250	0.483480	0.024*
C6	0.7048 (3)	−0.0316 (2)	0.55637 (14)	0.0185 (5)
H6	0.723861	−0.124959	0.553456	0.022*
C7	0.4091 (2)	0.0393 (2)	0.68452 (14)	0.0156 (4)
H7	0.333452	0.016491	0.719368	0.019*
C8	0.4453 (2)	0.1688 (2)	0.66264 (13)	0.0140 (4)
C9	0.3669 (2)	0.2839 (2)	0.68918 (13)	0.0142 (4)
H9	0.289165	0.270747	0.724287	0.017*
C10	0.3146 (2)	0.6275 (2)	0.67420 (13)	0.0133 (4)
C11	0.1947 (2)	0.7155 (2)	0.70049 (14)	0.0139 (4)
C12	0.1325 (2)	0.7050 (2)	0.77589 (14)	0.0156 (4)
H12	0.165590	0.641316	0.813786	0.019*
C13	0.0204 (2)	0.7902 (2)	0.79444 (14)	0.0185 (5)
H13	−0.021080	0.783377	0.846143	0.022*
C14	0.0301 (3)	0.8902 (2)	0.67103 (15)	0.0196 (5)
H14	−0.005725	0.954149	0.634104	0.023*
C15	0.1435 (2)	0.8117 (2)	0.64711 (15)	0.0168 (5)
H15	0.185233	0.823122	0.595771	0.020*
O1S	0.6541 (2)	0.6025 (2)	0.55370 (12)	0.0279 (4)
H1S	0.582293	0.623623	0.580387	0.042*
C1S	0.7704 (3)	0.5902 (2)	0.60520 (14)	0.0246 (5)
H1SA	0.757 (3)	0.4957 (4)	0.6166 (9)	0.037*
H1SB	0.776 (4)	0.6301 (9)	0.6581 (2)	0.037*
C2S	0.9016 (3)	0.5715 (3)	0.5560 (2)	0.0314 (6)
H2SA	0.889630	0.494186	0.520487	0.047*
H2SB	0.982242	0.556124	0.591660	0.047*
H2SC	0.918511	0.652049	0.523841	0.047*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0179 (8)	0.0109 (7)	0.0262 (8)	−0.0002 (6)	0.0061 (7)	−0.0001 (6)
N1	0.0189 (9)	0.0099 (8)	0.0183 (9)	−0.0004 (7)	0.0013 (7)	0.0009 (7)
N2	0.0137 (8)	0.0113 (8)	0.0169 (9)	0.0022 (7)	0.0002 (7)	−0.0012 (7)
N3	0.0120 (8)	0.0116 (8)	0.0177 (9)	0.0004 (7)	0.0025 (7)	−0.0003 (7)
N4	0.0150 (9)	0.0153 (9)	0.0282 (10)	0.0019 (8)	0.0009 (8)	−0.0020 (8)
C1	0.0156 (10)	0.0125 (10)	0.0147 (9)	−0.0009 (8)	−0.0034 (8)	0.0008 (8)
C2	0.0138 (10)	0.0122 (10)	0.0143 (9)	0.0011 (7)	−0.0018 (8)	−0.0001 (8)
C3	0.0182 (11)	0.0137 (10)	0.0178 (10)	−0.0015 (8)	0.0003 (9)	−0.0003 (8)
C4	0.0207 (11)	0.0219 (12)	0.0177 (10)	−0.0021 (10)	0.0046 (9)	0.0005 (9)
C5	0.0181 (11)	0.0250 (13)	0.0180 (10)	0.0025 (9)	0.0018 (9)	−0.0022 (9)
C6	0.0213 (11)	0.0158 (10)	0.0184 (11)	0.0043 (9)	−0.0012 (9)	−0.0016 (9)
C7	0.0168 (10)	0.0130 (10)	0.0171 (10)	0.0004 (8)	−0.0004 (8)	0.0005 (8)
C8	0.0139 (10)	0.0129 (10)	0.0153 (9)	−0.0004 (8)	−0.0011 (8)	0.0005 (8)
C9	0.0133 (9)	0.0135 (10)	0.0157 (10)	0.0000 (8)	0.0002 (8)	0.0003 (8)
C10	0.0138 (10)	0.0118 (9)	0.0143 (10)	0.0014 (8)	−0.0011 (8)	−0.0020 (8)
C11	0.0126 (9)	0.0110 (9)	0.0181 (10)	−0.0012 (8)	−0.0006 (8)	−0.0029 (8)
C12	0.0151 (10)	0.0134 (10)	0.0183 (10)	0.0001 (8)	−0.0004 (8)	−0.0007 (8)
C13	0.0165 (10)	0.0186 (10)	0.0204 (11)	−0.0007 (9)	0.0032 (9)	−0.0021 (9)
C14	0.0180 (10)	0.0144 (10)	0.0263 (11)	0.0018 (9)	−0.0003 (9)	0.0028 (9)
C15	0.0162 (10)	0.0132 (10)	0.0212 (11)	−0.0007 (8)	0.0006 (9)	0.0011 (8)
O1S	0.0224 (9)	0.0324 (10)	0.0288 (10)	0.0047 (8)	0.0065 (7)	−0.0004 (8)
C1S	0.0269 (13)	0.0223 (12)	0.0246 (12)	−0.0020 (10)	0.0061 (10)	−0.0072 (10)
C2S	0.0208 (12)	0.0312 (14)	0.0423 (16)	−0.0029 (11)	0.0077 (12)	−0.0042 (12)

Geometric parameters (Å, º) top

O1—C10	1.238 (3)	C7—C8	1.386 (3)
N1—C7	1.357 (3)	C7—H7	0.9500
N1—C1	1.381 (3)	C8—C9	1.437 (3)
N1—H1	0.8800	C9—H9	0.9500
N2—C9	1.292 (3)	C10—C11	1.501 (3)
N2—N3	1.396 (3)	C11—C12	1.393 (3)
N3—C10	1.339 (3)	C11—C15	1.396 (3)
N3—H3	0.8800	C12—C13	1.395 (3)
N4—C13	1.341 (3)	C12—H12	0.9500
N4—C14	1.346 (3)	C13—H13	0.9500
C1—C6	1.397 (3)	C14—C15	1.388 (3)
C1—C2	1.414 (3)	C14—H14	0.9500
C2—C3	1.401 (3)	C15—H15	0.9500
C2—C8	1.446 (3)	O1S—C1S	1.402 (3)
C3—C4	1.387 (3)	O1S—H1S	0.8400
C3—H3A	0.9500	C1S—C2S	1.500 (4)
C4—C5	1.411 (4)	C1S—H1SA	0.9700 (2)
C4—H4	0.9500	C1S—H1SB	0.9700 (2)
C5—C6	1.381 (3)	C2S—H2SA	0.9800
C5—H5	0.9500	C2S—H2SB	0.9800
C6—H6	0.9500	C2S—H2SC	0.9800

C7—N1—C1	109.00 (18)	N2—C9—H9	118.7
C7—N1—H1	125.5	C8—C9—H9	118.7
C1—N1—H1	125.5	O1—C10—N3	125.0 (2)
C9—N2—N3	112.49 (18)	O1—C10—C11	120.7 (2)
C10—N3—N2	119.74 (19)	N3—C10—C11	114.30 (19)
C10—N3—H3	120.1	C12—C11—C15	118.7 (2)
N2—N3—H3	120.1	C12—C11—C10	122.7 (2)
C13—N4—C14	116.9 (2)	C15—C11—C10	118.6 (2)
N1—C1—C6	129.1 (2)	C11—C12—C13	118.5 (2)
N1—C1—C2	108.2 (2)	C11—C12—H12	120.8
C6—C1—C2	122.6 (2)	C13—C12—H12	120.8
C3—C2—C1	119.3 (2)	N4—C13—C12	123.6 (2)
C3—C2—C8	134.4 (2)	N4—C13—H13	118.2
C1—C2—C8	106.20 (19)	C12—C13—H13	118.2
C4—C3—C2	118.1 (2)	N4—C14—C15	124.0 (2)
C4—C3—H3A	120.9	N4—C14—H14	118.0
C2—C3—H3A	120.9	C15—C14—H14	118.0
C3—C4—C5	121.6 (2)	C14—C15—C11	118.3 (2)
C3—C4—H4	119.2	C14—C15—H15	120.9
C5—C4—H4	119.2	C11—C15—H15	120.9
C6—C5—C4	121.3 (2)	C1S—O1S—H1S	109.5
C6—C5—H5	119.4	O1S—C1S—C2S	109.0 (2)
C4—C5—H5	119.4	O1S—C1S—H1SA	96.0 (14)
C5—C6—C1	117.0 (2)	C2S—C1S—H1SA	95.2 (13)
C5—C6—H6	121.5	O1S—C1S—H1SB	124.6 (19)
C1—C6—H6	121.5	C2S—C1S—H1SB	120 (2)
N1—C7—C8	110.3 (2)	H1SA—C1S—H1SB	103.2 (9)
N1—C7—H7	124.9	C1S—C2S—H2SA	109.5
C8—C7—H7	124.9	C1S—C2S—H2SB	109.5
C7—C8—C9	122.4 (2)	H2SA—C2S—H2SB	109.5
C7—C8—C2	106.3 (2)	C1S—C2S—H2SC	109.5
C9—C8—C2	131.2 (2)	H2SA—C2S—H2SC	109.5
N2—C9—C8	122.6 (2)	H2SB—C2S—H2SC	109.5

C9—N2—N3—C10	−177.7 (2)	C3—C2—C8—C9	0.1 (4)
C7—N1—C1—C6	179.6 (2)	C1—C2—C8—C9	−178.0 (2)
C7—N1—C1—C2	−1.0 (3)	N3—N2—C9—C8	174.45 (19)
N1—C1—C2—C3	−177.2 (2)	C7—C8—C9—N2	−178.1 (2)
C6—C1—C2—C3	2.2 (3)	C2—C8—C9—N2	−1.6 (4)
N1—C1—C2—C8	1.3 (2)	N2—N3—C10—O1	−3.5 (3)
C6—C1—C2—C8	−179.3 (2)	N2—N3—C10—C11	174.32 (18)
C1—C2—C3—C4	−1.8 (3)	O1—C10—C11—C12	−139.5 (2)
C8—C2—C3—C4	−179.8 (2)	N3—C10—C11—C12	42.5 (3)
C2—C3—C4—C5	−0.3 (4)	O1—C10—C11—C15	40.6 (3)
C3—C4—C5—C6	2.0 (4)	N3—C10—C11—C15	−137.4 (2)
C4—C5—C6—C1	−1.6 (4)	C15—C11—C12—C13	0.7 (3)
N1—C1—C6—C5	178.8 (2)	C10—C11—C12—C13	−179.2 (2)
C2—C1—C6—C5	−0.5 (3)	C14—N4—C13—C12	−1.1 (3)
C1—N1—C7—C8	0.2 (3)	C11—C12—C13—N4	0.7 (4)
N1—C7—C8—C9	177.8 (2)	C13—N4—C14—C15	0.0 (4)
N1—C7—C8—C2	0.6 (3)	N4—C14—C15—C11	1.4 (4)
C3—C2—C8—C7	177.1 (2)	C12—C11—C15—C14	−1.7 (3)
C1—C2—C8—C7	−1.1 (2)	C10—C11—C15—C14	178.2 (2)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···O1ⁱ	0.88	2.05	2.871 (3)	156
N3—H3···N4ⁱⁱ	0.88	2.14	2.979 (3)	159
C5—H5···N2ⁱⁱⁱ	0.95	2.62	3.236 (3)	123
O1S—H1S···O1	0.84	1.90	2.742 (3)	177

Symmetry codes: (i) x, y−1, z; (ii) −x, y−1/2, −z+3/2; (iii) x+1/2, −y+1/2, −z+1.

(2) (E)-N'-Methyl-2-[1-(2-oxo-2H-chromen-3-yl)ethylidene]hydrazinecarbothioamide top

Crystal data top

C₁₃H₁₃N₃O₂S	F(000) = 576
M_r = 275.32	D_x = 1.415 Mg m⁻³
Monoclinic, P2₁/c	Mo Kα radiation, λ = 0.71073 Å
a = 9.289 (4) Å	Cell parameters from 4293 reflections
b = 9.616 (4) Å	θ = 2.2–27.3°
c = 14.474 (6) Å	µ = 0.25 mm⁻¹
β = 90.825 (4)°	T = 100 K
V = 1292.8 (9) Å³	Block, yellow
Z = 4	0.49 × 0.46 × 0.31 mm

Data collection top

Bruker APEXII CCD diffractometer	2285 reflections with I > 2σ(I)
φ and ω scans	R_int = 0.044
Absorption correction: multi-scan (TWINABS; Bruker, 2012)	θ_max = 27.6°, θ_min = 2.2°
T_min = 0.534, T_max = 0.746	h = −12→12
5480 measured reflections	k = −12→12
2902 independent reflections	l = 0→18

Refinement top

Refinement on F²	0 restraints
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F² > 2σ(F²)] = 0.048	H-atom parameters constrained
wR(F²) = 0.116	w = 1/[σ²(F_o²) + (0.0375P)² + 0.711P] where P = (F_o² + 2F_c²)/3
S = 1.10	(Δ/σ)_max = 0.001
2902 reflections	Δρ_max = 0.30 e Å⁻³
174 parameters	Δρ_min = −0.35 e Å⁻³

Special details top

Experimental. For component 1: wR2(int) was 0.1337 before and 0.0605 after correction. The ratio of minimum to maximum transmission is 0.72. The λ/2 correction factor is not present

Final HKLF 4 output contains 20988 reflections, Rint = 0.0871 (9738 with I > 3sig(I), Rint = 0.0747)

Refinement. The absorption correction program TWINABS2 was employed to correct the data for absorption effects, as well as to separate hkl files for the domains with major component, which was used for further analysis.

1. Fixed Uiso; at 1.2 times of: All C(H) groups, all N(H) groups at 1.5 times of: all C(H, H, H) groups 2. a. Aromatic/amide H refined with riding coordinates: N2(H2), N3(H3), C3(H3A), C6(H6), C7(H7), C8(H8), C9(H9) b. Idealised Me refined as rotating group: C11(H11A, H11B, H11C), C13(H13A, H13B, H13C)

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
S1	0.80937 (6)	1.04558 (5)	0.39682 (4)	0.02114 (16)
O1	0.21617 (15)	0.36330 (14)	0.44249 (10)	0.0215 (3)
O2	0.37162 (18)	0.38370 (16)	0.33164 (11)	0.0314 (4)
N1	0.52878 (17)	0.75100 (17)	0.43518 (11)	0.0160 (4)
N2	0.61381 (18)	0.84670 (17)	0.39257 (11)	0.0173 (4)
H2	0.6171	0.8510	0.3319	0.021*
N3	0.67181 (19)	0.92800 (18)	0.53607 (11)	0.0197 (4)
H3	0.6007	0.8755	0.5554	0.024*
C1	0.3192 (2)	0.4382 (2)	0.39822 (14)	0.0200 (4)
C2	0.3575 (2)	0.5745 (2)	0.43650 (13)	0.0158 (4)
C3	0.3017 (2)	0.6138 (2)	0.51797 (13)	0.0164 (4)
H3A	0.3296	0.7005	0.5441	0.020*
C4	0.2019 (2)	0.5287 (2)	0.56577 (13)	0.0182 (4)
C5	0.1581 (2)	0.4043 (2)	0.52496 (14)	0.0193 (4)
C6	0.1375 (2)	0.5677 (2)	0.64904 (14)	0.0256 (5)
H6	0.1641	0.6528	0.6780	0.031*
C7	0.0363 (2)	0.4834 (3)	0.68876 (15)	0.0311 (6)
H7	−0.0071	0.5099	0.7452	0.037*
C8	−0.0026 (2)	0.3591 (3)	0.64601 (16)	0.0310 (6)
H8	−0.0720	0.3010	0.6743	0.037*
C9	0.0567 (2)	0.3179 (2)	0.56388 (15)	0.0256 (5)
H9	0.0289	0.2332	0.5349	0.031*
C10	0.4546 (2)	0.6670 (2)	0.38477 (13)	0.0164 (4)
C11	0.4552 (3)	0.6675 (3)	0.28152 (14)	0.0309 (6)
H11A	0.4431	0.7630	0.2590	0.046*
H11B	0.3760	0.6097	0.2579	0.046*
H11C	0.5470	0.6302	0.2599	0.046*
C12	0.6937 (2)	0.9357 (2)	0.44612 (13)	0.0159 (4)
C13	0.7581 (2)	1.0010 (2)	0.60437 (14)	0.0273 (5)
H13A	0.8603	0.9825	0.5938	0.041*
H13B	0.7326	0.9689	0.6663	0.041*
H13C	0.7399	1.1011	0.5994	0.041*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
S1	0.0185 (3)	0.0218 (3)	0.0231 (3)	−0.0043 (2)	0.0011 (2)	0.0012 (2)
O1	0.0192 (8)	0.0158 (7)	0.0295 (8)	−0.0012 (6)	−0.0026 (6)	−0.0015 (6)
O2	0.0320 (9)	0.0280 (9)	0.0343 (9)	−0.0001 (7)	0.0055 (7)	−0.0140 (7)
N1	0.0141 (8)	0.0183 (9)	0.0155 (8)	0.0000 (7)	−0.0004 (6)	0.0013 (6)
N2	0.0162 (8)	0.0225 (9)	0.0130 (8)	−0.0038 (7)	−0.0018 (6)	0.0010 (7)
N3	0.0206 (9)	0.0219 (9)	0.0164 (9)	−0.0043 (7)	−0.0021 (7)	−0.0015 (7)
C1	0.0168 (10)	0.0206 (11)	0.0226 (11)	0.0015 (9)	−0.0033 (8)	−0.0010 (9)
C2	0.0133 (9)	0.0178 (10)	0.0161 (10)	0.0009 (8)	−0.0036 (7)	−0.0009 (8)
C3	0.0138 (10)	0.0181 (10)	0.0173 (10)	0.0009 (8)	−0.0036 (7)	0.0001 (8)
C4	0.0138 (10)	0.0235 (11)	0.0171 (10)	0.0018 (8)	−0.0053 (7)	0.0054 (8)
C5	0.0140 (10)	0.0200 (10)	0.0237 (11)	0.0045 (8)	−0.0051 (8)	0.0066 (8)
C6	0.0212 (11)	0.0361 (13)	0.0195 (11)	−0.0010 (10)	−0.0027 (8)	0.0017 (9)
C7	0.0218 (12)	0.0522 (16)	0.0193 (11)	−0.0009 (11)	−0.0017 (9)	0.0119 (10)
C8	0.0171 (11)	0.0420 (14)	0.0339 (13)	−0.0039 (10)	−0.0045 (9)	0.0221 (11)
C9	0.0172 (11)	0.0237 (11)	0.0356 (13)	−0.0026 (9)	−0.0070 (9)	0.0114 (9)
C10	0.0149 (10)	0.0193 (10)	0.0151 (10)	0.0015 (8)	−0.0009 (7)	−0.0019 (8)
C11	0.0347 (14)	0.0419 (14)	0.0162 (11)	−0.0165 (11)	0.0014 (9)	−0.0042 (10)
C12	0.0131 (9)	0.0162 (10)	0.0184 (10)	0.0035 (8)	−0.0027 (7)	0.0008 (8)
C13	0.0269 (12)	0.0347 (13)	0.0202 (11)	−0.0033 (11)	−0.0069 (9)	−0.0041 (9)

Geometric parameters (Å, º) top

S1—C12	1.674 (2)	C4—C6	1.404 (3)
O1—C1	1.365 (2)	C5—C9	1.382 (3)
O1—C5	1.375 (3)	C6—C7	1.374 (3)
O2—C1	1.206 (2)	C6—H6	0.9500
N1—C10	1.282 (3)	C7—C8	1.392 (4)
N1—N2	1.366 (2)	C7—H7	0.9500
N2—C12	1.367 (3)	C8—C9	1.375 (3)
N2—H2	0.8800	C8—H8	0.9500
N3—C12	1.323 (3)	C9—H9	0.9500
N3—C13	1.446 (3)	C10—C11	1.494 (3)
N3—H3	0.8800	C11—H11A	0.9800
C1—C2	1.464 (3)	C11—H11B	0.9800
C2—C3	1.349 (3)	C11—H11C	0.9800
C2—C10	1.479 (3)	C13—H13A	0.9800
C3—C4	1.423 (3)	C13—H13B	0.9800
C3—H3A	0.9500	C13—H13C	0.9800
C4—C5	1.392 (3)

C1—O1—C5	122.86 (16)	C6—C7—H7	120.1
C10—N1—N2	118.48 (16)	C8—C7—H7	120.1
N1—N2—C12	118.61 (16)	C9—C8—C7	121.8 (2)
N1—N2—H2	120.7	C9—C8—H8	119.1
C12—N2—H2	120.7	C7—C8—H8	119.1
C12—N3—C13	123.65 (18)	C8—C9—C5	117.6 (2)
C12—N3—H3	118.2	C8—C9—H9	121.2
C13—N3—H3	118.2	C5—C9—H9	121.2
O2—C1—O1	116.07 (18)	N1—C10—C2	114.68 (17)
O2—C1—C2	126.37 (19)	N1—C10—C11	123.86 (18)
O1—C1—C2	117.55 (17)	C2—C10—C11	121.29 (17)
C3—C2—C1	119.16 (18)	C10—C11—H11A	109.5
C3—C2—C10	121.28 (18)	C10—C11—H11B	109.5
C1—C2—C10	119.56 (17)	H11A—C11—H11B	109.5
C2—C3—C4	121.67 (18)	C10—C11—H11C	109.5
C2—C3—H3A	119.2	H11A—C11—H11C	109.5
C4—C3—H3A	119.2	H11B—C11—H11C	109.5
C5—C4—C6	117.92 (19)	N3—C12—N2	115.66 (17)
C5—C4—C3	118.43 (18)	N3—C12—S1	124.32 (15)
C6—C4—C3	123.51 (19)	N2—C12—S1	120.02 (15)
O1—C5—C9	117.38 (19)	N3—C13—H13A	109.5
O1—C5—C4	119.94 (18)	N3—C13—H13B	109.5
C9—C5—C4	122.7 (2)	H13A—C13—H13B	109.5
C7—C6—C4	120.3 (2)	N3—C13—H13C	109.5
C7—C6—H6	119.9	H13A—C13—H13C	109.5
C4—C6—H6	119.9	H13B—C13—H13C	109.5
C6—C7—C8	119.7 (2)

C10—N1—N2—C12	−179.56 (18)	C5—C4—C6—C7	1.0 (3)
C5—O1—C1—O2	172.55 (18)	C3—C4—C6—C7	176.49 (19)
C5—O1—C1—C2	−6.3 (3)	C4—C6—C7—C8	−0.1 (3)
O2—C1—C2—C3	−171.9 (2)	C6—C7—C8—C9	−0.7 (3)
O1—C1—C2—C3	6.9 (3)	C7—C8—C9—C5	0.5 (3)
O2—C1—C2—C10	8.9 (3)	O1—C5—C9—C8	−179.46 (18)
O1—C1—C2—C10	−172.34 (17)	C4—C5—C9—C8	0.4 (3)
C1—C2—C3—C4	−2.7 (3)	N2—N1—C10—C2	−175.51 (16)
C10—C2—C3—C4	176.51 (17)	N2—N1—C10—C11	−0.1 (3)
C2—C3—C4—C5	−2.2 (3)	C3—C2—C10—N1	28.8 (3)
C2—C3—C4—C6	−177.73 (19)	C1—C2—C10—N1	−152.03 (18)
C1—O1—C5—C9	−178.67 (18)	C3—C2—C10—C11	−146.7 (2)
C1—O1—C5—C4	1.5 (3)	C1—C2—C10—C11	32.4 (3)
C6—C4—C5—O1	178.71 (18)	C13—N3—C12—N2	172.14 (19)
C3—C4—C5—O1	3.0 (3)	C13—N3—C12—S1	−8.2 (3)
C6—C4—C5—C9	−1.1 (3)	N1—N2—C12—N3	−5.4 (3)
C3—C4—C5—C9	−176.87 (18)	N1—N2—C12—S1	174.97 (13)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N2—H2···O2ⁱ	0.88	2.39	3.269 (3)	175
C11—H11A···O2ⁱ	0.98	2.47	3.109 (3)	123
C7—H7···S1ⁱⁱ	0.95	2.85	3.711 (3)	151
C11—H11B···S1ⁱⁱⁱ	0.98	2.87	3.728 (3)	146

Symmetry codes: (i) −x+1, y+1/2, −z+1/2; (ii) x−1, −y+3/2, z+1/2; (iii) −x+1, y−1/2, −z+1/2.

Acknowledgements

GD thanks the UGC–SAP and DST–FIST for funding to Centre of Advanced Study in Crystallography and Biophysics, University of Madras.

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CRYSTALLOGRAPHIC
COMMUNICATIONS

ISSN: 2056-9890

Volume 73| Part 4| April 2017| Pages 594-597

https://doi.org/10.1107/S205698901700411X

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research communications\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Crystal structures of the Schiff base derivatives (E)-N′-[(1H-indol-3-yl)methyl­­idene]isonicotino­hydrazide ethanol monosolvate and (E)-N-methyl-2-[1-(2-oxo-2H-chromen-3-yl)ethyl­­idene]hydrazinecarbo­thio­amide

1. Chemical context

2. Structural commentary

3. Supra­molecular features

4. Database survey

5. Synthesis and crystallization

6. Refinement

Supporting information

Acknowledgements

References

research communications

Crystal structures of the Schiff base derivatives (E)-N′-[(1H-indol-3-yl)methylidene]isonicotinohydrazide ethanol monosolvate and (E)-N-methyl-2-[1-(2-oxo-2H-chromen-3-yl)ethylidene]hydrazinecarbothioamide

3. Supramolecular features