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Acta Crystallographica Section E: Crystallographic Communications logoLink to Acta Crystallographica Section E: Crystallographic Communications
. 2021 May 11;77(Pt 6):596–599. doi: 10.1107/S2056989021004813

Crystal structure and Hirshfeld surface analysis of N-[(Z)-(2-hy­droxy­phen­yl)methyl­idene]aniline N-oxide

Shaaban K Mohamed a,b,*, Awad I Said c, Joel T Mague d, Moustafa F Aly e, Mehmet Akkurt f, Sahar M I Elgarhy g
PMCID: PMC8183447  PMID: 34164134

The conformation of the title compound is partially determined by a strong, intra­molecular O—H⋯O hydrogen bond. In the crystal, C—H⋯O hydrogen bonds link the mol­ecules, forming chains along the a-axis direction, which are linked into strongly corrugated sheets parallel to the ac plane by C—H⋯O hydrogen bonds and C—H⋯π(ring) inter­actions. The sheets are associated through additional C—H⋯π(ring) inter­actions.

Keywords: crystal structure, hydrogen bond, N-oxide, C—H⋯π(ring), nitrones, Hirshfeld surface analysis

Abstract

The conformation of the title compound, C13H11NO2, is partially determined by a strong, intra­molecular O—H⋯O hydrogen bond. The crystal packing consists of strongly corrugated layers parallel to the ac plane and associated through C—H⋯π(ring) inter­actions. A Hirshfeld surface analysis of the crystal structure indicates that the most significant contributions to the crystal packing are from H⋯H (44.1%), C⋯H/H⋯C (29.4%) and O⋯H/H⋯O (17.3%) contacts.

Chemical context  

Nitro­nes are a very important class of organic compounds as a result of their medicinal and pharmaceutical applications. They show anti­fungal (Salman et al., 2013), anti­bacterial (Chakraborty et al., 2010), neuroprotective (Chioua et al., 2012) and anti­cancer (Floyd et al., 2011) activities. In addition, nitrone compounds are widely used as anti­oxidant agents (Al-Mowali et al., 2014) because of their ability to scavenge free radicals. Based on these findings and following our inter­est in this area, we report herein the crystal structure of the title compound.graphic file with name e-77-00596-scheme1.jpg

Structural commentary  

The mol­ecular structure of the title compound (Fig. 1) is almost planar, with maximum deviations of 0.398 (2) Å for O1 and −0.756 (2) Å for O2. The N1—O2 distance of 1.331 (2) Å is normal for a single bond and agrees well with those observed in other amine N-oxides. The dihedral angle between the aromatic rings (C1–C6 and C8–C13) is 1.94 (12) °. The torsion angles C2—C1—C7—N1, C1—C7—N1—C8, C1—C7—N1—O2, C7—N1—C8—C9 and O2—N1—C8–C-9 are −30.2 (3), −179.7 (2), −0.4 (3), 27.3 (3) and −152.0 (2)°, respectively. The conformation of the title compound is partially determined by a strong, intra­molecular O1—H1⋯O2 hydrogen bond (Table 1).

Figure 1.

Figure 1

The title mol­ecule with labelling scheme and 50% probability ellipsoids. The intra­molecular hydrogen bond is shown by a dashed line.

Table 1. Hydrogen-bond geometry (Å, °).

Cg1 and Cg2 are the centroids of the C1–C6 and C8–C13 aromatic rings, respectively.

D—H⋯A D—H H⋯A DA D—H⋯A
O1—H1⋯O2 0.97 1.53 2.479 (2) 167
C7—H7⋯O2i 0.95 2.43 3.368 (3) 167
C10—H10⋯O1ii 0.95 2.53 3.227 (3) 131
C11—H11⋯Cg1iii 0.95 2.94 3.662 (3) 136
C4—H4⋯Cg2iv 0.95 2.77 3.545 (3) 140

Symmetry codes: (i) x-1, y, z; (ii) x-1, -y, z-{\script{1\over 2}}; (iii) x, -y, z-{\script{1\over 2}}; (iv) x, -y+1, z+{\script{1\over 2}}.

Supra­molecular features  

In the crystal, C7—H7⋯O2i hydrogen bonds (Table 1) link the mol­ecules, forming chains along the a-axis direction. The chains are linked into strongly corrugated sheets parallel to the ac plane by C10—H10⋯O2ii hydrogen bonds and C11—H11⋯Cg1iii inter­actions (Cg1 is the centroid of the C1–C6 hy­droxy­phenyl ring; Table 1 and Fig. 2). The sheets are stacked along the b-axis direction by C4—H4⋯Cg2iv inter­actions (Cg2 is the centroid of the C8–C13 phenyl ring; Table 1 and Figs. 2 and 3).

Figure 2.

Figure 2

Detail of the inter­molecular C—H⋯O hydrogen bonds and the C—H⋯π(ring) inter­actions (black and green dashed lines, respectively) viewed along the b-axis direction.

Figure 3.

Figure 3

Packing viewed along the (120) direction with inter­molecular inter­actions shown as in Fig. 2.

Hirshfeld surface analysis  

A Hirshfeld surface analysis (Spackman & Jayatilaka, 2009) was carried out using CrystalExplorer17.5 (Turner et al., 2017) to visualize the inter­molecular inter­actions in the title compound. The Hirshfeld surface mapped over d norm (Fig. 4) shows the expected bright-red spots near atoms O1, O2, H7 and H10, which are involved in the C—H⋯O hydrogen-bonding inter­actions. The bright-red spot near O1 indicates its role as a hydrogen-bond acceptor to (C10)H10 (Fig. 4) and another red region near O2 correlates with the C7—H7⋯O2 inter­action.

Figure 4.

Figure 4

A view of the three-dimensional Hirshfeld surface with the C—H⋯O inter­actions for the title compound, plotted over d norm in the range −0.2242 to 1.2146 a.u. (a) front view, (b) back view.

The two-dimensional fingerprint plots show the relative contributions of the various types of contacts to the Hirshfeld surface for the title compound (McKinnon et al., 2007). The plots (Fig. 5) reveal that H⋯H and C⋯H/H⋯C inter­actions make the greatest contributions to the surface contacts, while O⋯H/H⋯O, C⋯C, N⋯H/H⋯N, N⋯C/C⋯N and O⋯C/C⋯O contacts are less significant (Tables 2 and 3).

Figure 5.

Figure 5

A view of the two-dimensional fingerprint plots for the title compound, showing (a) all inter­actions, and delineated into (b) H⋯H, (c) C⋯H/H⋯C and (d) O⋯H/H⋯O inter­actions. The d i and d e values are the closest inter­nal and external distances (in Å) from given points on the Hirshfeld surface.

Table 2. Summary of short inter­atomic contacts (Å) in the title compound.

Contact Distance Symmetry operation
O2⋯H7 2.43 1 + x, y, z
O1⋯H10 2.53 1 + x, −y, {1\over 2} + z
O2⋯H12 2.87 x, 1 + y, z
C3⋯H12 3.02 x, −y, {1\over 2} + z
H4⋯C11 2.86 x, 1 − y, {1\over 2} + z
H6⋯H13 2.46 −1 + x, 1 + y, z

Table 3. Percentage contributions of inter­atomic contacts to the Hirshfeld surface for the title compound.

Contact Percentage contribution
H⋯H 44.1
C⋯H/H⋯C 29.4
O⋯H/H⋯O 17.3
C⋯C 5.3
N⋯C/C⋯N 1.7
N⋯H/H⋯N 1.5
O⋯C/C⋯O 0.7

Database survey  

The four most closely related structures are (Z)-N-[(1,3-diphenyl-1H-pyrazol-4-yl)methanimine]-N-oxido (DEPVOM; Mohamed et al., 2018), (Z)-1,2-bis­(3-bromo­phen­yl)diazene 1-oxide (SIYHAK01; Goswami et al., 2018), (Z)-N-benzyl­idene-1-phenyl­methanamine oxide hydrogen peroxide solvate (JELQOJ; Churakov et al., 2017) and (Z)-N-(2-chloro­benzyl­idene)aniline N-oxide (ERIXEJ; Fu et al., 2011).

In the crystal of DEPVOM, (101) layers are generated by C—H⋯O hydrogen bonds coupled with C—H⋯π(ring) and offset π–π stacking inter­actions. In the crystal of SIYHAK01, C—H⋯O and C—H⋯Br hydrogen bonds together with offset π–π inter­actions stack the mol­ecules along the a-axis direction. In the crystal of JELQOJ, the organic and peroxide mol­ecules are linked through both peroxide O—H donor groups to oxide O-atom acceptors, giving one-dimensional chains extending along the b-axis direction. Weak inter­molecular C—H⋯O hydrogen-bonding inter­actions are also present. In the crystal of ERIXEJ, the mol­ecule is stabilized by an intra­molecular C—H⋯O hydrogen bond. The geometry about the C=N bond is Z [C—C—N—O torsion angle = −4.2 (3)°] and the phenyl and benzene rings are trans-oriented around the C=N bond. The phenyl and benzene rings make a dihedral angle of 56.99 (2)°.

Synthesis and crystallization  

(Z)-(2-Hy­droxy­phen­yl)methyl­idene]benzenimine N-oxide (nitrone) was prepared according to the reported procedures (Mobinikhaledi et al., 2005). 0.7 ml (6 mmol) of salicyaldehyde were added to a warmed solution of 0.8 g (6 mmol) N-phenyl­hydroxy­amine in ethanol followed by stirring for 5 minutes, then standing at room temperature in the dark overnight gave the nitrone, which was recrystallized from ethanol in 53% yield; m.p. 387–388 K.

Refinement  

Crystal and refinement details are presented in Table 4. The H atom of the OH group was found in difference-Fourier maps, and its positional parameters were fixed using the AFIX 3 instruction in SHELXL and were refined with the isotropic displacement parameter U iso(H) = 1.5U eq(O). The C-bound H atoms were positioned geometrically, with C—H = 0.95 Å, and constrained to ride on their parent atoms, withU iso(H) = 1.2U eq(C). Attempts to determine the absolute structure did not produce a definitive result, viz.: Flack x = 0.2 (3) by classical fit to all intensities 0.30 (14) from 611 selected quotients (Parsons’ method). A round of TWIN/BASF refinement gave BASF = 0.2 (4) with no improvement in the model.

Table 4. Experimental details.

Crystal data
Chemical formula C13H11NO2
M r 213.23
Crystal system, space group Monoclinic, P c
Temperature (K) 150
a, b, c (Å) 5.5391 (1), 5.7873 (2), 16.0859 (4)
β (°) 99.067 (1)
V3) 509.21 (2)
Z 2
Radiation type Cu Kα
μ (mm−1) 0.77
Crystal size (mm) 0.19 × 0.17 × 0.15
 
Data collection
Diffractometer Bruker D8 VENTURE PHOTON 100 CMOS
Absorption correction Multi-scan (SADABS; Krause et al., 2015)
T min, T max 0.77, 0.89
No. of measured, independent and observed [I > 2σ(I)] reflections 3578, 1654, 1607
R int 0.023
(sin θ/λ)max−1) 0.618
 
Refinement
R[F 2 > 2σ(F 2)], wR(F 2), S 0.033, 0.084, 1.06
No. of reflections 1654
No. of parameters 145
No. of restraints 2
H-atom treatment H-atom parameters constrained
Δρmax, Δρmin (e Å−3) 0.18, −0.18
Absolute structure Flack x determined using 611 quotients [(I +)−(I )]/[(I +)+(I )] (Parsons et al., 2013).
Absolute structure parameter 0.30 (13)

Computer programs: APEX3 and SAINT (Bruker, 2016), SHELXT (Sheldrick, 2015a ), SHELXL (Sheldrick, 2015b ), ORTEP-3 for Windows (Farrugia, 2012), DIAMOND (Brandenburg & Putz, 2012) and PLATON (Spek, 2020).

Supplementary Material

Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S2056989021004813/ey2006sup1.cif

e-77-00596-sup1.cif (127.2KB, cif)

Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989021004813/ey2006Isup2.hkl

e-77-00596-Isup2.hkl (133.2KB, hkl)

Supporting information file. DOI: 10.1107/S2056989021004813/ey2006Isup3.cml

CCDC reference: 2082055

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

supplementary crystallographic information

Crystal data

C13H11NO2 F(000) = 224
Mr = 213.23 Dx = 1.391 Mg m3
Monoclinic, Pc Cu Kα radiation, λ = 1.54178 Å
a = 5.5391 (1) Å Cell parameters from 3430 reflections
b = 5.7873 (2) Å θ = 5.6–72.4°
c = 16.0859 (4) Å µ = 0.77 mm1
β = 99.067 (1)° T = 150 K
V = 509.21 (2) Å3 Block, yellow
Z = 2 0.19 × 0.17 × 0.15 mm

Data collection

Bruker D8 VENTURE PHOTON 100 CMOS diffractometer 1654 independent reflections
Radiation source: INCOATEC IµS micro–focus source 1607 reflections with I > 2σ(I)
Mirror monochromator Rint = 0.023
Detector resolution: 10.4167 pixels mm-1 θmax = 72.4°, θmin = 5.6°
ω scans h = −6→6
Absorption correction: multi-scan (SADABS; Krause et al., 2015) k = −7→7
Tmin = 0.77, Tmax = 0.89 l = −19→19
3578 measured reflections

Refinement

Refinement on F2 Hydrogen site location: mixed
Least-squares matrix: full H-atom parameters constrained
R[F2 > 2σ(F2)] = 0.033 w = 1/[σ2(Fo2) + (0.0441P)2 + 0.084P] where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.084 (Δ/σ)max < 0.001
S = 1.06 Δρmax = 0.18 e Å3
1654 reflections Δρmin = −0.18 e Å3
145 parameters Absolute structure: Flack x determined using 611 quotients [(I+)-(I-)]/[(I+)+(I-)] (Parsons et al., 2013).
2 restraints Absolute structure parameter: 0.30 (13)

Special details

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)

x y z Uiso*/Ueq
O1 0.8449 (3) 0.3532 (3) 0.64513 (12) 0.0342 (4)
H1 0.841875 0.289527 0.589214 0.051*
O2 0.7828 (3) 0.2215 (3) 0.49662 (12) 0.0338 (4)
N1 0.5424 (3) 0.1864 (3) 0.48272 (13) 0.0267 (4)
C1 0.4520 (4) 0.4953 (4) 0.57874 (14) 0.0260 (5)
C2 0.6705 (4) 0.5169 (4) 0.63617 (15) 0.0280 (5)
C3 0.7030 (4) 0.7093 (4) 0.68930 (16) 0.0328 (5)
H3 0.852651 0.728354 0.726592 0.039*
C4 0.5207 (5) 0.8717 (4) 0.68821 (18) 0.0348 (5)
H4 0.545906 1.001606 0.724635 0.042*
C5 0.3009 (4) 0.8470 (4) 0.63443 (17) 0.0349 (6)
H5 0.174797 0.958261 0.634589 0.042*
C6 0.2662 (4) 0.6611 (4) 0.58092 (16) 0.0304 (5)
H6 0.114410 0.643651 0.544695 0.036*
C7 0.3908 (4) 0.3082 (4) 0.51888 (15) 0.0270 (5)
H7 0.222390 0.270734 0.504648 0.032*
C8 0.4586 (4) 0.0034 (4) 0.42327 (14) 0.0263 (5)
C9 0.2257 (4) 0.0070 (4) 0.37527 (15) 0.0304 (5)
H9 0.116018 0.130115 0.380872 0.036*
C10 0.1571 (4) −0.1720 (4) 0.31930 (17) 0.0340 (5)
H10 −0.001169 −0.171673 0.286384 0.041*
C11 0.3176 (5) −0.3521 (4) 0.31083 (16) 0.0327 (5)
H11 0.269918 −0.473587 0.271973 0.039*
C12 0.5480 (5) −0.3533 (4) 0.35956 (18) 0.0324 (5)
H12 0.657396 −0.477040 0.354374 0.039*
C13 0.6199 (4) −0.1748 (4) 0.41587 (16) 0.0301 (5)
H13 0.778043 −0.175337 0.448865 0.036*

Atomic displacement parameters (Å2)

U11 U22 U33 U12 U13 U23
O1 0.0260 (9) 0.0382 (9) 0.0363 (9) 0.0038 (6) −0.0010 (7) 0.0001 (7)
O2 0.0137 (7) 0.0461 (9) 0.0418 (9) −0.0015 (7) 0.0047 (7) −0.0028 (8)
N1 0.0170 (9) 0.0340 (9) 0.0290 (10) −0.0013 (7) 0.0031 (7) 0.0025 (8)
C1 0.0253 (12) 0.0287 (11) 0.0250 (12) −0.0010 (8) 0.0073 (10) 0.0032 (8)
C2 0.0232 (12) 0.0314 (11) 0.0301 (12) 0.0004 (8) 0.0057 (10) 0.0066 (9)
C3 0.0308 (13) 0.0359 (12) 0.0320 (12) −0.0082 (10) 0.0059 (10) −0.0024 (10)
C4 0.0380 (14) 0.0300 (11) 0.0397 (13) −0.0066 (9) 0.0166 (11) −0.0022 (10)
C5 0.0346 (14) 0.0328 (12) 0.0403 (15) 0.0032 (9) 0.0150 (11) 0.0065 (10)
C6 0.0232 (11) 0.0362 (12) 0.0321 (12) 0.0026 (9) 0.0054 (9) 0.0071 (10)
C7 0.0185 (10) 0.0327 (11) 0.0293 (11) 0.0009 (8) 0.0028 (9) 0.0049 (9)
C8 0.0241 (11) 0.0292 (11) 0.0258 (13) −0.0022 (8) 0.0044 (10) 0.0029 (8)
C9 0.0218 (11) 0.0379 (12) 0.0316 (13) 0.0017 (9) 0.0053 (10) −0.0012 (9)
C10 0.0246 (11) 0.0448 (13) 0.0329 (12) −0.0037 (9) 0.0052 (10) −0.0013 (11)
C11 0.0328 (12) 0.0340 (12) 0.0328 (13) −0.0066 (9) 0.0096 (10) −0.0021 (10)
C12 0.0336 (12) 0.0307 (11) 0.0341 (12) 0.0044 (9) 0.0096 (10) 0.0023 (10)
C13 0.0249 (11) 0.0350 (12) 0.0307 (13) 0.0025 (8) 0.0056 (9) 0.0053 (9)

Geometric parameters (Å, º)

O1—C2 1.345 (3) C5—H5 0.9500
O1—H1 0.9697 C6—H6 0.9500
O2—N1 1.331 (2) C7—H7 0.9500
N1—C7 1.302 (3) C8—C13 1.382 (3)
N1—C8 1.454 (3) C8—C9 1.395 (3)
C1—C2 1.407 (3) C9—C10 1.386 (4)
C1—C6 1.411 (3) C9—H9 0.9500
C1—C7 1.453 (3) C10—C11 1.391 (4)
C2—C3 1.398 (4) C10—H10 0.9500
C3—C4 1.377 (4) C11—C12 1.389 (4)
C3—H3 0.9500 C11—H11 0.9500
C4—C5 1.385 (4) C12—C13 1.390 (4)
C4—H4 0.9500 C12—H12 0.9500
C5—C6 1.372 (4) C13—H13 0.9500
C2—O1—H1 105.1 N1—C7—C1 126.9 (2)
C7—N1—O2 122.78 (18) N1—C7—H7 116.6
C7—N1—C8 121.79 (18) C1—C7—H7 116.6
O2—N1—C8 115.43 (17) C13—C8—C9 121.2 (2)
C2—C1—C6 118.6 (2) C13—C8—N1 117.2 (2)
C2—C1—C7 125.97 (19) C9—C8—N1 121.66 (19)
C6—C1—C7 115.4 (2) C10—C9—C8 118.9 (2)
O1—C2—C3 118.3 (2) C10—C9—H9 120.5
O1—C2—C1 122.5 (2) C8—C9—H9 120.5
C3—C2—C1 119.1 (2) C9—C10—C11 120.6 (2)
C4—C3—C2 120.8 (2) C9—C10—H10 119.7
C4—C3—H3 119.6 C11—C10—H10 119.7
C2—C3—H3 119.6 C12—C11—C10 119.6 (2)
C3—C4—C5 120.5 (2) C12—C11—H11 120.2
C3—C4—H4 119.7 C10—C11—H11 120.2
C5—C4—H4 119.7 C11—C12—C13 120.5 (2)
C6—C5—C4 119.6 (2) C11—C12—H12 119.8
C6—C5—H5 120.2 C13—C12—H12 119.8
C4—C5—H5 120.2 C8—C13—C12 119.2 (2)
C5—C6—C1 121.2 (2) C8—C13—H13 120.4
C5—C6—H6 119.4 C12—C13—H13 120.4
C1—C6—H6 119.4
C6—C1—C2—O1 172.1 (2) C6—C1—C7—N1 153.4 (2)
C7—C1—C2—O1 −4.2 (3) C7—N1—C8—C13 −153.0 (2)
C6—C1—C2—C3 −4.4 (3) O2—N1—C8—C13 27.7 (3)
C7—C1—C2—C3 179.3 (2) C7—N1—C8—C9 27.3 (3)
O1—C2—C3—C4 −174.0 (2) O2—N1—C8—C9 −152.0 (2)
C1—C2—C3—C4 2.6 (3) C13—C8—C9—C10 −0.1 (3)
C2—C3—C4—C5 0.1 (4) N1—C8—C9—C10 179.6 (2)
C3—C4—C5—C6 −1.0 (4) C8—C9—C10—C11 −0.2 (4)
C4—C5—C6—C1 −0.9 (4) C9—C10—C11—C12 0.6 (4)
C2—C1—C6—C5 3.6 (3) C10—C11—C12—C13 −0.7 (4)
C7—C1—C6—C5 −179.7 (2) C9—C8—C13—C12 0.0 (3)
O2—N1—C7—C1 −0.4 (3) N1—C8—C13—C12 −179.8 (2)
C8—N1—C7—C1 −179.7 (2) C11—C12—C13—C8 0.4 (4)
C2—C1—C7—N1 −30.2 (3)

Hydrogen-bond geometry (Å, º)

Cg1 and Cg2 are the centroids of the C1–C6 and C8–C13 aromatic rings, respectively.

D—H···A D—H H···A D···A D—H···A
O1—H1···O2 0.97 1.53 2.479 (2) 167
C7—H7···O2i 0.95 2.43 3.368 (3) 167
C10—H10···O1ii 0.95 2.53 3.227 (3) 131
C11—H11···Cg1iii 0.95 2.94 3.662 (3) 136
C4—H4···Cg2iv 0.95 2.77 3.545 (3) 140

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

Funding Statement

This work was funded by National Science Foundation grant 1228232. Tulane University grant .

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Associated Data

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

Supplementary Materials

Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S2056989021004813/ey2006sup1.cif

e-77-00596-sup1.cif (127.2KB, cif)

Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989021004813/ey2006Isup2.hkl

e-77-00596-Isup2.hkl (133.2KB, hkl)

Supporting information file. DOI: 10.1107/S2056989021004813/ey2006Isup3.cml

CCDC reference: 2082055

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


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

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