Crystallographic and spectroscopic characterization of 3-chloro-5-fluoro­salicyl­aldehyde

Triggs, C.T.; Tanski, J.M.

doi:10.1107/S2056989020014425

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ISSN: 2056-9890

Volume 76| Part 12| December 2020| Pages 1810-1812

https://doi.org/10.1107/S2056989020014425

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Crystallographic and spectroscopic characterization of 3-chloro-5-fluorosalicylaldehyde

Christopher T. Triggs ^a and Joseph M. Tanski ^a ^*

^aDepartment of Chemistry, Vassar College, Poughkeepsie, NY 12604, USA
^*Correspondence e-mail: jotanski@vassar.edu

Edited by S. Parkin, University of Kentucky, USA (Received 23 October 2020; accepted 29 October 2020; online 3 November 2020)

The title compound (systematic name: 3-chloro-5-fluoro-2-hydroxybenzaldehyde), C₇H₄ClFO₂, is a dihalogenated salicylaldehyde derivative that has been studied for its antibacterial characteristics. The salicylaldehyde engages in intramolecular hydrogen bonding with an O—H⋯O distance of 2.6231 (19) Å while the molecules pack together via weak intermolecular C—H⋯O, C—H⋯F and F⋯O interactions and offset face-to-face π-stacking.

Keywords: crystal structure; hydrogen bonding; halogenated salicylaldehyde derivative.

CCDC reference: 2041401

1. Chemical context

Salicylaldehyde and its derivatives, including the title compound 3-chloro-5-fluoro-2-hydroxybenzaldehyde, (I), play an important role in the synthesis of novel antimicrobial complexes (Bozkır et al., 2012 ; Dahlgren et al., 2010 ; Sarı et al., 2013 ). The title compound, commonly known as 3-chloro-5-fluorosalicylaldehyde, may be synthesized by the formylation of 2-chloro-4-fluorophenol with chloroform through reflux with concentrated NaOH(aq) (Balko et al., 2007 ).

2. Structural commentary

The molecular structure of the title compound (Fig. 1) is planar, with an r.m.s. deviation from the plane of all non-hydrogen atoms of 0.0135 Å. The molecule engages in intramolecular hydrogen bonding between the phenol hydrogen atom and formyl functional group oxygen with an O1⋯O2 distance of 2.6231 (19) Å characterizing the O1—H1⋯O2 interaction. The C3—Cl and C5—F bond lengths were found to be 1.7334 (16) and 1.3529 (19) Å, respectively.

Figure 1
A view of 3-chloro-5-fluorosalicylaldehyde, (I)

, depicting the intramolecular hydrogen bonding with the atom-numbering scheme. Displacement ellipsoids are shown at the 50% probability level.

3. Supramolecular features

The molecules pack together in the solid state with weak intermolecular C—H⋯O, C—H⋯F and F⋯O interactions and an offset face-to-face π-stacking geometrical relationship. Molecules of 3-chloro-5-fluorosalicylaldehyde form one-dimensional π-stacking chains (Fig. 2), which are characterized by a ring centroid-to-centroid distance of 3.7154 (3) Å, a centroid-to-plane distance of 3.3989 (8) Å, and a ring-offset slippage of 1.501 (2) Å. These π-stacking chains are linked together to form the three-dimensional structure through weak intermolecular C—H⋯O and C—H⋯F contacts (Table 1 and Fig. 3). Specifically, O1—H1⋯Fⁱ, C4—H4A⋯O2ⁱⁱ, and C6—H6A⋯O1ⁱⁱⁱ intermolecular interactions (symmetry codes as defined in Table 1), with donor–acceptor distances of 3.0101 (18), 3.254 (2) and 3.377 (2) Å, respectively. In addition, an O2⋯Fⁱ contact with a distance of 2.880 (2) Å is observed. Notably, there are no close halogen–halogen interactions.

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O1—H1⋯Fⁱ	0.77 (3)	2.47 (3)	3.0101 (18)	128 (2)
O1—H1⋯O2	0.77 (3)	1.93 (3)	2.6231 (19)	150 (3)
C4—H4A⋯O2ⁱⁱ	0.95	2.37	3.254 (2)	155
C6—H6A⋯O1ⁱⁱⁱ	0.95	2.55	3.377 (2)	145
Symmetry codes: (i) $[-x+{\script{1\over 2}}, y-{\script{1\over 2}}, z-{\script{1\over 2}}]$ ; (ii) $[x+{\script{1\over 2}}, -y+{\script{1\over 2}}, z+1]$ ; (iii) $[-x+{\script{1\over 2}}, y+{\script{1\over 2}}, z-{\script{1\over 2}}]$ .

Figure 2
A view of the intermolecular π-stacking in 3-chloro-5-fluorosalicylaldehyde, (I)

, with the thick line indicating a centroid-to-centroid relationship.

Figure 3
A view of the packing and weak intermolecular C—H⋯O, C—H⋯F and F⋯O interactions in 3-chloro-5-fluorosalicylaldehyde, (I)

. Symmetry codes are defined in Table 1

4. Database survey

The Cambridge Structural Database (Version 5.40, update of March 2020; Groom et al., 2016 ) contains many halogenated benzene structures and relatively few halogenated salicylaldehyde structures. Literature aryl C—Cl and C—F bond lengths, as seen in halogenated benzene crystal structures, are similar to those seen in the title compound. For example, the C—Cl distances in 1,2- and 1,3-dichlorobenzene range between 1.731 (3) and 1.756 (3) Å (ABUMIT and ABUMOZ; Boese et al., 2001 ), while the C—F distances in 1,3-difluorobenzene are found to be between 1.3486 (14) and 1.3553 (13) Å (PUGDAX; Kirchner et al., 2009 ). Related salicylaldehyde structures that differ in the number of halogen atoms include unsubstituted salicylaldehyde itself (YADJOE; Kirchner et al., 2011 ), 5-chlorosalicylaldehyde (RAJGOA01; Aitken et al., 2013 ; RAJGOA, Jin et al., 2011 ), and 3,5-dichlorosalicylaldehyde (MIXYEY; Azizul & Ng, 2008 ). As with the title compound, each of these structures exhibits strong intramolecular hydrogen bonding between the phenol hydrogen atom and formyl oxygen atom.

5. Synthesis and crystallization

3-Chloro-5-fluorosalicylaldehyde (I, 97%) was purchased from Aldrich Chemical Company, USA, and was used as received.

6. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2. All non-hydrogen atoms were refined anisotropically. Hydrogen atoms bonded to carbon were included in calculated positions and refined using a riding model with C—H = 0.95 and U_iso(H) = 1.2U_eq(C) for the aryl H atoms. The position of the phenolic hydrogen atom was found in the difference map and refined freely.

Table 2
Experimental details

Crystal data
Chemical formula	C₇H₄ClFO₂
M_r	174.55
Crystal system, space group	Orthorhombic, Pna2₁
Temperature (K)	125
a, b, c (Å)	14.2730 (13), 12.7102 (12), 3.7154 (3)
V (Å³)	674.02 (10)
Z	4
Radiation type	Mo Kα
μ (mm⁻¹)	0.52
Crystal size (mm)	0.45 × 0.10 × 0.02

Data collection
Diffractometer	Bruker APEXII CCD
Absorption correction	Multi-scan (SADABS; Bruker, 2017 )
T_min, T_max	0.87, 0.99
No. of measured, independent and observed [I > 2σ(I)] reflections	16131, 2052, 1985
R_int	0.030
(sin θ/λ)_max (Å⁻¹)	0.715

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.023, 0.066, 1.07
No. of reflections	2052
No. of parameters	104
No. of restraints	1
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.34, −0.19
Absolute structure	Flack x determined using 837 quotients [(I⁺)−(I⁻)]/[(I⁺)+(I⁻)] (Parsons et al., 2013 )
Absolute structure parameter	0.07 (2)
Computer programs: APEX2 and SAINT (Bruker, 2017), SHELXT2014/5 (Sheldrick, 2015a ), SHELXL2017/1 (Sheldrick, 2015b ), SHELXTL (Sheldrick, 2008 ), OLEX2 (Dolomanov et al., 2009 ), and Mercury (Macrae et al., 2020 ).

7. Analytical Data

¹H NMR (Bruker Avance III 400 MHz, CDCl₃): δ 7.23 (dd, 1H, C_arylH, J_meta = 3.0 Hz, J_H–F = 7.2 Hz), 7.42 (dd, 1H, C_arylH, J_meta = 3.0 Hz, J_H–F = 7.8 Hz), 9.86 (s, 1H, OH), 11.21 (s, 1H, C(=O)H). ¹³C NMR (¹³C{¹H}, 100.6 MHz, CDCl₃): δ 116.90 (d, C_arylH, J_C–F = 22.6 Hz), 120.24 (d, C_aryl, J_C–F = 6.6 Hz), 123.15 (d, C_aryl, J_C–F = 9.1 Hz), 124.72 (d, C_arylH, J_C–F = 26.4 Hz), 153.85 (d, C_aryl, J_C–F = 2.2 Hz), 154.85 (d, C_arylF, J_C–F = 244.0 Hz), 194.97 (C(=O)H). ¹⁹F NMR (¹⁹F{¹H}, 376.5 MHz, CDCl₃): δ −121.50. IR (Thermo Nicolet iS50, ATR, cm⁻¹) : 3081 (m br, O—H & C_aryl—H str), 2859 [w, C(=O)—H fermi doublet str], 2733 [w, C(=O)—H fermi doublet str], 1803 (w), 1754 (w), 1664 (s, C=O str), 1623 (m), 1583 (w), 1524 (w), 1462 (m), 1436 (s), 1373 (m), 1351 (w), 1294 (s), 1238 (s), 1183 (s), 1119 (s), 982 (s), 902 (m), 894 (m), 875 (s), 802 (s), 727 (s), 708 (s), 578 (m), 530 (s), 493 (s), 458 (m). GC/MS (Agilent MS 5975/GC 7890): M⁺ = 174 (calc. exact mass 173.99).

Supporting information

CCDC reference: 2041401

Crystal structure: contains datablocks global, I. DOI: https://doi.org/10.1107/S2056989020014425/pk2651sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989020014425/pk2651Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2056989020014425/pk2651Isup3.cml

checkCIF report

Computing details top

Data collection: APEX2 (Bruker, 2017); cell refinement: SAINT (Bruker, 2017); data reduction: SAINT (Bruker, 2017); program(s) used to solve structure: SHELXT2014/5 (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2017/1 (Sheldrick, 2015b); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008), OLEX2 (Dolomanov et al., 2009), and Mercury (Macrae et al., 2020).

3-Chloro-5-fluoro-2-hydroxybenzaldehyde top

Crystal data top

C₇H₄ClFO₂	D_x = 1.720 Mg m⁻³
M_r = 174.55	Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, Pna2₁	Cell parameters from 9931 reflections
a = 14.2730 (13) Å	θ = 2.9–30.5°
b = 12.7102 (12) Å	µ = 0.52 mm⁻¹
c = 3.7154 (3) Å	T = 125 K
V = 674.02 (10) Å³	Needle, colourless
Z = 4	0.45 × 0.10 × 0.02 mm
F(000) = 352

Data collection top

Bruker APEXII CCD diffractometer	2052 independent reflections
Radiation source: fine-focus sealed tube	1985 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.030
Detector resolution: 8.3333 pixels mm^-1	θ_max = 30.5°, θ_min = 2.2°
φ and ω scans	h = −20→20
Absorption correction: multi-scan (SADABS; Bruker, 2017)	k = −18→17
T_min = 0.87, T_max = 0.99	l = −5→5
16131 measured reflections

Refinement top

Refinement on F²	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: mixed
R[F² > 2σ(F²)] = 0.023	H atoms treated by a mixture of independent and constrained refinement
wR(F²) = 0.066	w = 1/[σ²(F_o²) + (0.0394P)² + 0.1224P] where P = (F_o² + 2F_c²)/3
S = 1.07	(Δ/σ)_max < 0.001
2052 reflections	Δρ_max = 0.34 e Å⁻³
104 parameters	Δρ_min = −0.19 e Å⁻³
1 restraint	Absolute structure: Flack x determined using 837 quotients [(I⁺)-(I^-)]/[(I⁺)+(I^-)] (Parsons et al., 2013)
Primary atom site location: dual	Absolute structure parameter: 0.07 (2)

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
Cl	0.43892 (3)	0.11149 (3)	0.78847 (17)	0.02049 (11)
F	0.41791 (7)	0.50784 (8)	0.7158 (3)	0.0246 (3)
O1	0.25167 (10)	0.12611 (10)	0.4770 (4)	0.0204 (3)
H1	0.202 (2)	0.137 (2)	0.412 (8)	0.036 (8)*
O2	0.11001 (9)	0.23221 (11)	0.2114 (4)	0.0256 (3)
C1	0.24600 (12)	0.31544 (12)	0.4365 (4)	0.0143 (3)
C2	0.29149 (11)	0.22104 (12)	0.5277 (4)	0.0142 (3)
C3	0.38146 (11)	0.22705 (12)	0.6760 (4)	0.0141 (3)
C4	0.42463 (11)	0.32301 (13)	0.7379 (4)	0.0157 (3)
H4A	0.485639	0.326265	0.8395	0.019*
C5	0.37672 (11)	0.41404 (13)	0.6482 (5)	0.0160 (3)
C6	0.28892 (11)	0.41307 (13)	0.4973 (4)	0.0157 (3)
H6A	0.258084	0.476816	0.435752	0.019*
C7	0.15263 (10)	0.31310 (13)	0.2738 (6)	0.0186 (3)
H7A	0.123791	0.378134	0.213767	0.022*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Cl	0.02085 (18)	0.01654 (18)	0.02407 (19)	0.00416 (13)	−0.00540 (17)	0.00218 (18)
F	0.0206 (5)	0.0149 (5)	0.0384 (7)	−0.0046 (4)	−0.0032 (5)	−0.0033 (5)
O1	0.0189 (6)	0.0142 (6)	0.0281 (7)	−0.0017 (5)	−0.0059 (5)	0.0005 (5)
O2	0.0192 (5)	0.0225 (6)	0.0350 (9)	−0.0014 (5)	−0.0094 (6)	−0.0006 (5)
C1	0.0138 (7)	0.0147 (7)	0.0145 (6)	0.0007 (5)	−0.0012 (5)	0.0000 (6)
C2	0.0156 (7)	0.0133 (7)	0.0136 (6)	−0.0007 (5)	−0.0007 (6)	0.0000 (6)
C3	0.0153 (7)	0.0133 (7)	0.0139 (6)	0.0024 (5)	−0.0015 (5)	0.0006 (5)
C4	0.0141 (6)	0.0165 (7)	0.0166 (8)	0.0001 (5)	−0.0005 (6)	−0.0012 (6)
C5	0.0160 (7)	0.0135 (7)	0.0185 (7)	−0.0025 (6)	0.0011 (6)	−0.0017 (6)
C6	0.0167 (7)	0.0136 (7)	0.0167 (7)	0.0011 (6)	0.0001 (6)	0.0005 (6)
C7	0.0162 (7)	0.0192 (7)	0.0205 (7)	0.0022 (5)	−0.0031 (7)	0.0008 (8)

Geometric parameters (Å, º) top

Cl—C3	1.7334 (16)	C2—C3	1.399 (2)
F—C5	1.3529 (19)	C3—C4	1.386 (2)
O1—C2	1.3470 (19)	C4—C5	1.385 (2)
O1—H1	0.77 (3)	C4—H4A	0.95
O2—C7	1.217 (2)	C5—C6	1.373 (2)
C1—C6	1.402 (2)	C6—H6A	0.95
C1—C2	1.406 (2)	C7—H7A	0.95
C1—C7	1.464 (2)

C2—O1—H1	106 (2)	C5—C4—H4A	120.8
C6—C1—C2	120.99 (14)	C3—C4—H4A	120.8
C6—C1—C7	118.83 (14)	F—C5—C6	118.71 (15)
C2—C1—C7	120.18 (14)	F—C5—C4	118.49 (14)
O1—C2—C3	119.41 (14)	C6—C5—C4	122.79 (15)
O1—C2—C1	122.42 (14)	C5—C6—C1	118.19 (15)
C3—C2—C1	118.17 (14)	C5—C6—H6A	120.9
C4—C3—C2	121.43 (14)	C1—C6—H6A	120.9
C4—C3—Cl	119.70 (12)	O2—C7—C1	123.44 (15)
C2—C3—Cl	118.87 (12)	O2—C7—H7A	118.3
C5—C4—C3	118.42 (15)	C1—C7—H7A	118.3

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O1—H1···Fⁱ	0.77 (3)	2.47 (3)	3.0101 (18)	128 (2)
O1—H1···O2	0.77 (3)	1.93 (3)	2.6231 (19)	150 (3)
C4—H4A···O2ⁱⁱ	0.95	2.37	3.254 (2)	155
C6—H6A···O1ⁱⁱⁱ	0.95	2.55	3.377 (2)	145

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

Funding information

This work was supported by Vassar College. X-ray facilities were provided by the US National Science Foundation (grants Nos. 0521237 and 0911324 to JMT). We acknowledge the Salmon Fund and Olin College Fund of Vassar College for funding publication expenses.

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