Crystal structure and Hirshfeld surface analysis of (E)-2-cyano-N′-(3,4,5-tri­meth­oxy­benzyl­idene)acetohydrazide

Maheswari, S.U.; Senthilkumar, S.; Selvanayagam, S.

doi:10.1107/S2056989025003913

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Volume 81| Part 6| June 2025|

https://doi.org/10.1107/S2056989025003913

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Crystal structure and Hirshfeld surface analysis of (E)-2-cyano-N′-(3,4,5-trimethoxybenzylidene)acetohydrazide

Subramani Uma Maheswari,^a,^b Srinivasan Senthilkumar ^a ^* and Sivashanmugam Selvanayagam ^c ‡

^aDepartment of Chemistry, Annamalai University, Annamalainagar, Chidambaram 608 002, India, ^bDepartment of Science and Humanities, Rathinam Technical Campus, Coimbatore 641 021, India, and ^cPG & Research Department of Physics, Government Arts College, Melur 625 106, India
^*Correspondence e-mail: senraj05@gmail.com

Edited by B. Therrien, University of Neuchâtel, Switzerland (Received 23 April 2025; accepted 1 May 2025; online 9 May 2025)

In the title compound, C₁₃H₁₅N₃O₄, the 2-cyano-N′-methylideneacetohydrazide moiety and the trimethoxy phenol ring form a dihedral angle of 13.8 (1)°. Intermolecular N—H⋯O and C—H⋯O hydrogen bonds are observed. The intermolecular interactions were quantified and analysed using Hirshfeld surface analysis, revealing that H⋯H interactions contribute most to the crystal packing (38.3%).

Keywords: benzohydrazine; intermolecular hydrogen bonds; Hirshfeld surface analysis; crystal structure.

CCDC reference: 2448154

1. Chemical context

Hydrazones have been found to show various biological properties, including anticonvulsant (Angelova et al., 2016 ), antifungal (Ozdemir et al., 2008 ) and antitumoral (Parlar et al., 2018 ). In the present work, the synthesis, structural and computational studies of (E)-2-cyano-N′-(3,4,5-trimethoxybenzylidene)acetohydrazide, (I), are reported.

2. Structural commentary

The molecular structure of (I) is displayed in Fig. 1. The phenyl ring (C1–C6) is planar with a maximum deviation of 0.008 (2) Å for atom C6 and its attached methoxy atoms O1, C11, O2, C12, O3 and C13 deviate by 0.023 (2), −0.169 (4), 0.133 (2), −1.089 (3), 0.010 (2) and 0.056 (3) Å, respectively. The 2-cyano-N′-methylideneacetohydrazide moiety (C7/N1/N2/C8/O4/C9/C10/N3) is nearly planar with a maximum deviation of 0.280 (3) Å for atom N3. This moiety forms a dihedral angle of 13.8 (1)° with the trimethoxy phenyl ring.

Figure 1
A view of the molecular structure of compound (I)

, showing the atom labelling. Displacement ellipsoids are drawn at the 30% probability level.

3. Supramolecular features

In the crystal, molecules associate pairwise by C9—H9B⋯O2ⁱ and C13—H13A⋯O4ⁱ hydrogen bonds (Table 1) into inversion dimers with an R₂² (22) graph-set motifs (Etter et al., 1990 ), as shown in Fig. 2. The molecules are further linked into a C(4) chain motif by N2—H2⋯O4ⁱⁱⁱ hydrogen bonds running parallel to [0 $[\overline{1}]$ 0] (Table 1; Fig. 3).

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
C9—H9B⋯O2ⁱ	0.97	2.50	3.448 (3)	165
C13—H13A⋯O4ⁱⁱ	0.96	2.51	3.350 (3)	146
N2—H2⋯O4ⁱⁱⁱ	0.86	1.98	2.802 (3)	160
Symmetry codes: (i) ; (ii) ; (iii) $[x, -y+{\script{1\over 2}}, z-{\script{1\over 2}}]$ .

Figure 2
A view of the dimeric arrangement through O—H⋯O hydrogen bonds

Figure 3
The crystal packing of the title compound (I)

viewed along the b axis. The N—H⋯O and O—H⋯O intermolecular hydrogen bonds are shown as dashed lines. For clarity, H atoms not involved in hydrogen bonds have been omitted.

4. Hirshfeld surface analysis

To further characterize the intermolecular interactions, we carried out a Hirshfeld surface (HS) analysis (Spackman & Jayatilaka, 2009 ) using Crystal Explorer 21 (Spackman et al., 2021 ) The HS mapped over d_norm is illustrated in Fig. 4 where the deep-red spot occurs at O4 and this oxygen atom is responsible for intermolecular N—H⋯O and C—H⋯O hydrogen bonds.

Figure 4
A view of the Hirshfeld surface mapped over d_norm.

The associated two-dimensional fingerprint plots (McKinnon et al., 2007 ) provide quantitative information about the non-covalent interactions in the crystal packing in terms of the percentage contribution of the interatomic contacts (Spackman & McKinnon, 2002 ). The overall two-dimensional fingerprint plot is shown in Fig. 5a. The HS analysis reveals that H⋯H and H⋯O/O⋯H contacts are the main contributors to the crystal packing, followed by H⋯N/N⋯H, H⋯C/C⋯H, O⋯C/C⋯O and C⋯N/N⋯C contacts; see Fig. 5b–g. The HS analysis confirms the importance of H-atom contacts in the crystal (Hathwar et al., 2015 ).

Figure 5
Two-dimensional fingerprint plots for compound (I)

, showing (a) all interactions, and delineated into (b) H⋯H, (c) H⋯O/O⋯H, (d) H⋯N/N⋯H, (e)H⋯C/C⋯H, (f) O⋯C/C⋯O and (g) N⋯C/C⋯N interactions. The d_i and d_e values are the closest internal and external distances (in Å) from given points on the Hirshfeld surface.

5. Synthesis and crystallization

The title compound (I) was synthesized by condensing 2-cyano acetohydrazide in methanol with 3,4,5-trimethoxybenzaldehyde in a 1:1 ratio following an established protocol (Shaik et al., 2019 ). The progress of the reaction was monitored by thin layer chromatography (TLC). After completion of the reaction, methanol was removed under vacuum. The solid product was collected, washed, and recrystallized from methanol to obtain crystals of (I).

6. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2. All H atoms were placed in idealized positions and allowed to ride on their parent atoms: N—H = 0.86 and C—H = 0.93–0.97 Å, with U_iso(H) = 1.5U_eq(C) for methyl H atoms and U_iso(H) = 1.2U_eq(C, N) for all other H atoms.

Table 2
Experimental details

Crystal data
Chemical formula	C₁₃H₁₅N₃O₄
M_r	277.28
Crystal system, space group	Monoclinic, P2₁/c
Temperature (K)	298
a, b, c (Å)	13.9944 (8), 11.0371 (7), 9.0560 (5)
β (°)	99.936 (2)
V (Å³)	1377.79 (14)
Z	4
Radiation type	Mo Kα
μ (mm⁻¹)	0.10
Crystal size (mm)	0.16 × 0.12 × 0.08

Data collection
Diffractometer	Bruker APEXII CCD
Absorption correction	Multi-scan (SADABS; Krause et al., 2015 )
T_min, T_max	0.624, 0.745
No. of measured, independent and observed [I > 2σ(I)] reflections	23917, 2823, 1540
R_int	0.072
(sin θ/λ)_max (Å⁻¹)	0.625

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.053, 0.156, 1.05
No. of reflections	2823
No. of parameters	181
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.15, −0.23
Computer programs: APEX3 and SAINT (Bruker, 2017 ), SHELXT2018/2 (Sheldrick, 2015a ), SHELXL2019/2 (Sheldrick, 2015b ), ORTEP-3 for Windows (Farrugia, 2012 ) and PLATON (Spek, 2020 ).

Supporting information

CCDC reference: 2448154

Crystal structure: contains datablocks I, global. DOI: https://doi.org/10.1107/S2056989025003913/tx2097sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989025003913/tx2097Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2056989025003913/tx2097Isup3.cml

checkCIF report

Computing details top

(E)-2-Cyano-N'-(3,4,5-trimethoxybenzylidene)acetohydrazide top

Crystal data top

C₁₃H₁₅N₃O₄	F(000) = 584
M_r = 277.28	D_x = 1.337 Mg m⁻³
Monoclinic, P2₁/c	Mo Kα radiation, λ = 0.71073 Å
a = 13.9944 (8) Å	Cell parameters from 4885 reflections
b = 11.0371 (7) Å	θ = 2.4–22.9°
c = 9.0560 (5) Å	µ = 0.10 mm⁻¹
β = 99.936 (2)°	T = 298 K
V = 1377.79 (14) Å³	Block, brown
Z = 4	0.16 × 0.12 × 0.08 mm

Data collection top

Bruker APEXII CCD diffractometer	1540 reflections with I > 2σ(I)
Radiation source: i-mu-s microfocus source	R_int = 0.072
φ and ω scans	θ_max = 26.4°, θ_min = 2.4°
Absorption correction: multi-scan (SADABS; Krause et al., 2015)	h = −17→15
T_min = 0.624, T_max = 0.745	k = −13→13
23917 measured reflections	l = −11→8
2823 independent reflections

Refinement top

Refinement on F²	0 restraints
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F² > 2σ(F²)] = 0.053	H-atom parameters constrained
wR(F²) = 0.156	w = 1/[σ²(F_o²) + (0.0585P)² + 0.5215P] where P = (F_o² + 2F_c²)/3
S = 1.05	(Δ/σ)_max < 0.001
2823 reflections	Δρ_max = 0.15 e Å⁻³
181 parameters	Δρ_min = −0.23 e Å⁻³

Special details top

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.

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

	x	y	z	U_iso*/U_eq
O1	0.17230 (13)	0.43960 (19)	−0.1731 (2)	0.0708 (6)
O2	0.15221 (12)	0.52233 (16)	0.0935 (2)	0.0574 (5)
O3	0.29283 (12)	0.49755 (17)	0.3328 (2)	0.0586 (5)
O4	0.73449 (12)	0.30054 (17)	0.34803 (19)	0.0589 (5)
C7	0.51086 (18)	0.3277 (2)	0.0177 (3)	0.0473 (6)
H7	0.522223	0.308137	−0.077620	0.057*
N1	0.57857 (14)	0.31831 (18)	0.1302 (2)	0.0471 (5)
N3	0.98039 (19)	0.2939 (3)	0.3950 (3)	0.0824 (9)
C1	0.33918 (18)	0.3770 (2)	−0.0817 (3)	0.0502 (7)
H1	0.347981	0.349974	−0.175678	0.060*
C2	0.25037 (18)	0.4247 (2)	−0.0625 (3)	0.0496 (7)
C3	0.23722 (17)	0.4649 (2)	0.0780 (3)	0.0463 (6)
C4	0.31260 (18)	0.4556 (2)	0.1992 (3)	0.0458 (6)
C5	0.40109 (18)	0.4078 (2)	0.1801 (3)	0.0485 (7)
H5	0.451361	0.401270	0.261518	0.058*
C6	0.41465 (17)	0.3697 (2)	0.0388 (3)	0.0456 (6)
N2	0.66924 (14)	0.28820 (18)	0.1029 (2)	0.0446 (5)
H2	0.678178	0.272351	0.013346	0.054*
C8	0.74341 (17)	0.2840 (2)	0.2180 (3)	0.0423 (6)
C9	0.84027 (16)	0.2566 (2)	0.1732 (3)	0.0470 (6)
H9A	0.841502	0.172809	0.141281	0.056*
H9B	0.848985	0.307709	0.089430	0.056*
C10	0.9189 (2)	0.2776 (3)	0.2976 (3)	0.0533 (7)
C11	0.1728 (2)	0.3876 (3)	−0.3140 (4)	0.0847 (10)
H11A	0.112939	0.406117	−0.379339	0.127*
H11B	0.226071	0.419600	−0.355726	0.127*
H11C	0.179561	0.301281	−0.303628	0.127*
C12	0.0851 (2)	0.4491 (3)	0.1573 (4)	0.0719 (9)
H12A	0.028134	0.495629	0.164137	0.108*
H12B	0.067467	0.379559	0.094810	0.108*
H12C	0.114932	0.422970	0.255613	0.108*
C13	0.3689 (2)	0.4940 (3)	0.4573 (3)	0.0677 (8)
H13A	0.346330	0.525646	0.543898	0.102*
H13B	0.389969	0.411839	0.476062	0.102*
H13C	0.422169	0.542265	0.436720	0.102*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0544 (12)	0.0881 (15)	0.0646 (13)	0.0106 (10)	−0.0047 (10)	−0.0052 (11)
O2	0.0438 (10)	0.0538 (11)	0.0771 (13)	0.0103 (9)	0.0176 (9)	0.0081 (9)
O3	0.0502 (11)	0.0717 (13)	0.0553 (12)	0.0109 (9)	0.0128 (9)	−0.0084 (9)
O4	0.0594 (12)	0.0831 (14)	0.0376 (10)	0.0069 (10)	0.0184 (9)	0.0000 (9)
C7	0.0466 (15)	0.0463 (15)	0.0517 (16)	0.0016 (12)	0.0157 (13)	−0.0031 (12)
N1	0.0398 (12)	0.0527 (13)	0.0522 (13)	0.0056 (10)	0.0179 (11)	−0.0005 (10)
N3	0.0639 (17)	0.116 (2)	0.0637 (17)	−0.0227 (16)	0.0017 (14)	0.0100 (16)
C1	0.0499 (16)	0.0494 (15)	0.0522 (16)	0.0017 (12)	0.0110 (14)	−0.0042 (12)
C2	0.0438 (15)	0.0492 (15)	0.0534 (17)	0.0003 (12)	0.0020 (13)	0.0048 (13)
C3	0.0364 (14)	0.0400 (14)	0.0635 (18)	0.0024 (11)	0.0110 (13)	0.0062 (12)
C4	0.0460 (15)	0.0413 (14)	0.0521 (16)	0.0025 (11)	0.0138 (13)	0.0018 (12)
C5	0.0419 (15)	0.0508 (16)	0.0527 (16)	0.0048 (12)	0.0081 (12)	0.0020 (12)
C6	0.0432 (15)	0.0416 (14)	0.0532 (16)	0.0016 (11)	0.0118 (13)	−0.0011 (12)
N2	0.0410 (12)	0.0567 (13)	0.0396 (12)	0.0047 (10)	0.0162 (10)	−0.0017 (10)
C8	0.0432 (15)	0.0455 (14)	0.0407 (15)	0.0005 (11)	0.0141 (12)	0.0024 (11)
C9	0.0421 (15)	0.0551 (16)	0.0447 (15)	0.0009 (12)	0.0105 (12)	0.0021 (12)
C10	0.0477 (17)	0.0650 (18)	0.0497 (17)	−0.0052 (14)	0.0156 (14)	0.0077 (14)
C11	0.076 (2)	0.099 (3)	0.070 (2)	0.0001 (19)	−0.0110 (18)	−0.021 (2)
C12	0.0469 (17)	0.071 (2)	0.101 (2)	−0.0049 (15)	0.0221 (17)	0.0050 (18)
C13	0.072 (2)	0.078 (2)	0.0522 (18)	0.0183 (17)	0.0077 (16)	−0.0050 (15)

Geometric parameters (Å, º) top

O1—C2	1.359 (3)	C5—C6	1.390 (3)
O1—C11	1.401 (3)	C5—H5	0.9300
O2—C3	1.376 (3)	N2—C8	1.339 (3)
O2—C12	1.434 (3)	N2—H2	0.8600
O3—C4	1.367 (3)	C8—C9	1.511 (3)
O3—C13	1.412 (3)	C9—C10	1.451 (4)
O4—C8	1.219 (3)	C9—H9A	0.9700
C7—N1	1.270 (3)	C9—H9B	0.9700
C7—C6	1.467 (3)	C11—H11A	0.9600
C7—H7	0.9300	C11—H11B	0.9600
N1—N2	1.375 (3)	C11—H11C	0.9600
N3—C10	1.136 (3)	C12—H12A	0.9600
C1—C6	1.384 (3)	C12—H12B	0.9600
C1—C2	1.388 (3)	C12—H12C	0.9600
C1—H1	0.9300	C13—H13A	0.9600
C2—C3	1.389 (4)	C13—H13B	0.9600
C3—C4	1.389 (3)	C13—H13C	0.9600
C4—C5	1.384 (3)

C2—O1—C11	119.5 (2)	O4—C8—N2	123.5 (2)
C3—O2—C12	114.76 (19)	O4—C8—C9	122.4 (2)
C4—O3—C13	117.24 (19)	N2—C8—C9	114.1 (2)
N1—C7—C6	119.7 (2)	C10—C9—C8	110.8 (2)
N1—C7—H7	120.1	C10—C9—H9A	109.5
C6—C7—H7	120.1	C8—C9—H9A	109.5
C7—N1—N2	117.3 (2)	C10—C9—H9B	109.5
C6—C1—C2	120.1 (2)	C8—C9—H9B	109.5
C6—C1—H1	120.0	H9A—C9—H9B	108.1
C2—C1—H1	120.0	N3—C10—C9	179.9 (4)
O1—C2—C1	125.2 (2)	O1—C11—H11A	109.5
O1—C2—C3	114.8 (2)	O1—C11—H11B	109.5
C1—C2—C3	119.9 (2)	H11A—C11—H11B	109.5
O2—C3—C4	120.4 (2)	O1—C11—H11C	109.5
O2—C3—C2	119.6 (2)	H11A—C11—H11C	109.5
C4—C3—C2	119.8 (2)	H11B—C11—H11C	109.5
O3—C4—C5	124.2 (2)	O2—C12—H12A	109.5
O3—C4—C3	115.6 (2)	O2—C12—H12B	109.5
C5—C4—C3	120.2 (2)	H12A—C12—H12B	109.5
C4—C5—C6	119.8 (2)	O2—C12—H12C	109.5
C4—C5—H5	120.1	H12A—C12—H12C	109.5
C6—C5—H5	120.1	H12B—C12—H12C	109.5
C1—C6—C5	120.1 (2)	O3—C13—H13A	109.5
C1—C6—C7	120.5 (2)	O3—C13—H13B	109.5
C5—C6—C7	119.3 (2)	H13A—C13—H13B	109.5
C8—N2—N1	118.96 (19)	O3—C13—H13C	109.5
C8—N2—H2	120.5	H13A—C13—H13C	109.5
N1—N2—H2	120.5	H13B—C13—H13C	109.5

C6—C7—N1—N2	−174.8 (2)	O2—C3—C4—C5	−174.0 (2)
C11—O1—C2—C1	10.5 (4)	C2—C3—C4—C5	0.8 (4)
C11—O1—C2—C3	−171.3 (3)	O3—C4—C5—C6	−178.7 (2)
C6—C1—C2—O1	178.0 (2)	C3—C4—C5—C6	0.3 (4)
C6—C1—C2—C3	−0.1 (4)	C2—C1—C6—C5	1.3 (4)
C12—O2—C3—C4	−81.8 (3)	C2—C1—C6—C7	−175.5 (2)
C12—O2—C3—C2	103.3 (3)	C4—C5—C6—C1	−1.4 (4)
O1—C2—C3—O2	−4.3 (3)	C4—C5—C6—C7	175.4 (2)
C1—C2—C3—O2	174.0 (2)	N1—C7—C6—C1	−178.0 (2)
O1—C2—C3—C4	−179.2 (2)	N1—C7—C6—C5	5.1 (4)
C1—C2—C3—C4	−1.0 (4)	C7—N1—N2—C8	176.4 (2)
C13—O3—C4—C5	1.6 (4)	N1—N2—C8—O4	3.2 (4)
C13—O3—C4—C3	−177.5 (2)	N1—N2—C8—C9	−176.8 (2)
O2—C3—C4—O3	5.1 (3)	O4—C8—C9—C10	−11.6 (3)
C2—C3—C4—O3	180.0 (2)	N2—C8—C9—C10	168.4 (2)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C9—H9B···O2ⁱ	0.97	2.50	3.448 (3)	165
C13—H13A···O4ⁱⁱ	0.96	2.51	3.350 (3)	146
N2—H2···O4ⁱⁱⁱ	0.86	1.98	2.802 (3)	160

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

Footnotes

‡Additional correspondence author, e-mail: sselvanayagam@gmail.com.

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