Synthesis, Characterization, and Crystal Structure of (2E)-3-(4-Fluorophenyl)-1-(2-hydroxyphenyl)prop-2-en-1-one

Article abstract of DOI:10.1007/s10870-018-0732-4

The title chalcone, of formula C₁₅H₁₁F₁O_2, crystallized in the orthorhombic space group P2₁2₁2₁ (# 19) with crystal parameters a = 6.9998(8) ?, b = 12.6740(15) ?, c = 12.8997(15)

Full text of DOI:10.1007/s10870-018-0732-4

Journal of Chemical Crystallography
https://doi.org/10.1007/s10870-018-0732-4
ORIGINAL PAPER
Synthesis, Characterization, and Crystal Structure of (2E)-3-(4-
Fluorophenyl)-1-(2-hydroxyphenyl)prop-2-en-1-one
Cathryn A. Slabber1 · Craig D. Grimmer2 · Orde Q. Munro1 · Ross S. Robinson2
Received: 23 February 2015 / Accepted: 7 September 2018
© Springer Science+Business Media, LLC, part of Springer Nature 2018
Abstract
The title chalcone, of formula C15H11F1O2, crystallized in the orthorhombic space group P212121 (# 19) with crystal param-
eters a = 6.9998(8) Å, b = 12.6740(15) Å, c = 12.8997(15) Å, V = 1144.4(2) Å3, Z = 4, determined at 100 K with MoKα
radiation. The solid-state structure displays an intramolecular S(6) hydrogen bond and the crystal architecture is maintained
by intermolecular F⋯H, O⋯H, and C⋯C short contacts. A DFT geometry optimization is compared with the experimental
structure. As 19F NMR spectroscopy can be used for metabolic tagging of biologically active compounds (including chal-
cones), the solution-state 19F chemical shift and 13C19F coupling constants (nJ) are also reported.
Graphical Abstract
Keywords Chalcone · Hydrogen-bonding · DFT
Introduction
condensation of aldehydes and ketones with usually sponta-
neous dehydration of the ß-hydroxy ketone intermediate to
form a conjugated enone. The title fluorinated chalcone [3,
4] has been prepared as an intermediate in the preparation of
a novel range of cyclooxygenase (COX) inhibitors [5]. Fluo-
rine atoms are found in 20–30% of modern drugs [6] and the
inclusion of a fluorine atom in a pharmaceutical candidate
not only allows the modification of electrostatic properties
[7] but is also a means of metabolic tagging for study via
19F NMR spectroscopy. Fluorine atoms can also impart a
number of pharmaceutically appealing attributes to a drug
[8]. Herein we report the synthesis and characterization of
(2E)-3-(4-fluorophenyl)-1-(2-hydroxyphenyl)prop-2-en-1-
one by multiple spectroscopic methods and a combination
of single crystal X-ray diffraction and DFT simulations for
Chalcones are a class of natural products and synthetic
compounds with a wide range of biological activities [1].
They are readily prepared by the base-catalysed Aldol [2]
Electronic supplementary material The online version of this
article (https://doi.org/10.1007/s10870-018-0732-4) contains
supplementary material, which is available to authorized users.
* Ross S. Robinson
robinsonr@ukzn.ac.za
1
School of Chemistry, University of the Witwatersrand,
Johannesburg, South Africa
2
School of Chemistry and Physics, University
of KwaZulu-Natal, Pietermaritzburg, South Africa
Vol.:(0123456789)
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Journal of Chemical Crystallography
structure elucidation and delineation of the electronic and
magnetic properties of the compound.
Scheme 1 Basic synthesis of title chalcone
Experimental
Measurements (NMR Spectroscopy)
NMR data were recorded on either a Bruker Avance-III 500
or Bruker Avance-III 400 spectrometer with 1H freqencies of
500 MHz or 400 MHz, respectively, using a 5 mm 31P109Ag/
{1H} BBOZ probe. Data acquisition and processing were
carried out with Bruker TopSpin software (v 2.1, pl 6). All
proton and carbon chemical shifts are quoted in parts-per-
million (ppm) and are measured relative to the position of
1
the relevant solvent signal (DMSO-d6, H 2.50 ppm, 13C
Fig. 1 Intramolecular S(6) hydrogen bond; chalcone ring nomencla-
ture (A and B rings)
39.50 ppm) [9]. Coupling constants are reported in Hertz
(Hz). All experiments were performed at 30 °C.
Measurements (X‑ray Diffraction)
uncorrected). Translucent yellow crystals suitable for X-ray
diffraction were obtained by slow evaporation of an ethanol
solution. A SciFinder [23] search reveals 61 reports of the
synthesis of this compound between 2001 [24] and 2018
[25] and yet the crystal structure is not present in the Cam-
bridge Structural Database (May 2018).
A suitable single crystal was suspended in Paratone [10] oil
in a Mitegen [11] loop. X-ray diffraction data were collected
with a Bruker Apex Duo diffractometer with an Incoatec
IµS source [12] using Mo-Kα radiation at a temperature
of 100 K. The structure was solved with Olex2 [13] by
“Direct Methods” using ShelXS-1997 [14] and refined with
ShelXL-1997 [14] using CGLS minimisation. Absorption
correction was performed with SADABS [15]. Molecular
measurements were determined with Olex2 [13], Mercury
[16, 17], MacroModel [18, 19] and molecular visuals were
created with Olex2 [13], PyMol [20] and POVRay [21]. The
title chalcone is asymmetric, lacking any symmetry ele-
ments, permitting its crystallization in space group P212121.
The nonplanar conformation of the asymmetric unit coupled
with its absence of point chirality leads to its crystalliza-
tion in a chiral space group. The absolute structure is not
particularly relevant in the present case. However, the Flack
parameter [22] was refined, as is customary in ShelXL for
all chiral space groups, to give the correct absolute structure
(enantiomer) within the standard uncertainty of the estimate.
1H NMR, DMSO-d6 (assignments labelled as in Fig. 1):
δ 6.99–7.01 (m, 1 H, B3); 6.99–7.03 (m, 1 H, B5), 7.29–7.34
(m, 2 H, A3); 7.55–7.59 (m, 1 H, B4); 7.84 (d, 3JHH =15.6,
1 H, 3); 7.98–8.01 (m, 3 H, A2 and 2); 8.25 (dd, J=8.5 Hz,
J=1.6 Hz, 1 H, B6); 12.48 (br.s, 1 H, OH).
13C NMR, DMSOd6 (assignments labelled as in Fig. 1):
δ 115.95 (d, 2JCF =21.8 Hz, A3); 117.68 (s, B3); 119.10 (s,
B5); 120.66 (s, B1); 121.62 (d, 6JCF =2.3 Hz, 2); 130.83 (s,
B6); 131.10 (d, 4JCF =3.1 Hz, A1); 131.51 (d, 3JCF =8.7 Hz,
A2); 136.29 (s, B4); 143.52 (d, 5JCF =0.8 Hz, 3); 161.82 (s,
B2); 163.57 (d, 1JCF =249.7 Hz, A4); 193.52 (s, 1).
19F-{1H} NMR (DMSOd6): δ 109.0 (s, 1 F, F).
HRMS: Calculated C15H11O2F1 242.0743; found
241.0667 (M-1).
Results and Discussion
Synthesis and Characterisation
The summary of the single crystal diffraction data is pre-
sented in Table 1.
Potassium hydroxide (0.662 g; 11.2 mmol) was added to
ethanol (95%; 20 ml) and stirred until dissolved. To the solu-
tion was added slowly 2′-hydroxyacetophenone (0.549 g;
4.00 mmol), followed by 4-fluorobenzaldehyde (0.500 g;
4.00 mmol). The solution was stirred overnight at room tem-
perature. Hydrochloric acid (2.0 M) was added to neutralize
the solution and the yellow precipitate was isolated by suc-
tion filtration and allowed to air-dry overnight (Scheme 1)
with a yield of 80% (melting point 116.5–118.5 °C;
The molecular structure features a single intramolecular
hydrogen bond O2–H2⋯O1, generating an S(6) ring motif
[26, 27] (Fig. 1) with an angle between the plane of the S(6)
ring and that of the B ring [28] of the chalcone of 1.4 (3)°.
The intramolecular hydrogen bond is maintained in
solution, given the chemical shift of the phenolic proton at
12.48 ppm.
1 3

Journal of Chemical Crystallography
Table 1 Summary of crystal data
the A and B rings are 175.35 (10)° (C2C1C7C8), 169.03
(11)° (C1C7C8C9), and 164.92 (12)° (C8C9C10C11) cul-
minating in a twisted, non-planar structure. The fluoro- and
hydroxyl- substituents are placed on opposite sides of the
molecule and the double bond of the propene fragment
(C8C9) has an E- or trans-configuration (Fig. 2).
Formula
C15H11F1O2
Formula mass (g/mol)
Crystal system
Space group
a (Å)
b (Å)
c (Å)
242.24 (242.0743)
Orthorhombic
P212121 (# 19)
6.9998 (8)
12.6740 (15)
12.8997 (15)
90
The E/trans configuration of the propene fragment is con-
firmed by the 3JHH coupling constant of 15.6 Hz [29] in the
solution-state NMR spectrum.
α, β, γ (°)
V (Å3)
1144.4 (2)
4
Z
Temperature (K)
Radiation
Wavelength
Collected reflections
2Θ range (°)
Unique reflections
Rint
100 (2)
Mo Kα
0.71073
6675
4.506, 56.504
2790
0.0155
Rsigma
R1 (I>2σ(I))
wR2
0.0196
0.0296 (3%)
0.0824
Fig. 4 Head-to-tail stacking of columns, viewed along the b-axis
Flack parameter
Crystal size (mm)
Crystal description
0.0(2)
0.2×0.2×0.2
Clear, yellow shard
Fig. 2 Crystallographic atom labels; intramolecular S(6) H-bond; rel-
ative positions of the fluoro- and hydroxyl-substituents; configuration
of alkene bond. Thermal ellipsoids at 50%
Fig. 3 The five short contacts of the intermolecular structure
The angle between the planes of the hydroxyl-substituted
B ring and fluoro-substituted A ring of the chalcone is 29.88
(4)° and the torsion angles between the propene bridge and
Fig. 5 Staggered arrangement of columns, coloured by symmetry
operation, viewed along the a-axis
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Journal of Chemical Crystallography
The bulk structure is characterized by five short con-
tacts (Fig. 3): an F···H contact of 2.575 (1) Å, between
the fluorine atom and H15 of the A ring, an O⋯H contact
of 2.477 (2) Å between the oxygen atom of the carbonyl
moiety (O1) and H3 of the B ring, an O⋯H contact of
2.522 (2) Å between the oxygen atom of the hydroxyl
moiety (O2) and H6 of the B ring, a C⋯C contact of
3.318 (2) Å between the carbon atom of the carbonyl
group (C7) and C15 of the A ring, and a C⋯C contact
of 3.376 (2) Å between C11 of the A ring and C6 of the
B ring.
between the A and B rings and the carbonyl group maintain-
ing the columns. The planes of the A and B rings in each
layer are not quite coplanar, with a between-plane angle of
4.16 (4)°, and a between-centroid spacing of 3.7837 (8) Å.
Molecules are stacked in columns along the a axis (vis-
ible by viewing along the b axis; Fig. 4) in a slightly offset
head-to-tail arrangement, with the two C⋯C short contacts
Fig. 8 Superposition (all atoms) of CSD (blue) and HAR (green)
structures. RMSD 0.0864; maximum difference at atom H4
Table 3 H–X and H⋯X bond lengths
Bond (Å)
No HAR
HAR
O2–H2
O1⋯H2
C3–H3
C4–H4
C5–H5
C6–H6
C8–H8
C9–H9
C11–H11
C12–H12
C14–H14
C15–H15
0.852 (19)
1.75 (2)
0.987 (10)
1.613 (10)
1.088 (7)
1.118 (8)
1.088 (7)
1.056 (7)
1.075 (8)
1.094 (7)
1.087 (7)
1.072 (9)
1.081 (8)
1.068 (8)
0.95007 (8)
0.95004 (11)
0.95002 (9)
0.95005 (8)
0.94990 (10)
0.95003 (10)
0.95006 (10)
0.94998 (10)
0.95008 (10)
0.95008 (10)
Fig. 6 Hydrogen bonding network of head-to-head O⋯H short con-
tacts
Table 2 Crystal packing short contacts
Contact
Distance (Å)
Operations
C7–C15
C6–C11
H6–O2
F1–H15
O1–H3
3.318 (2)
3.376 (2)
2.522 (2)
2.575 (1)
2.477 (2)
1/2+x, 3/2−y, 1−z
1/2+x, 3/2−y, 1−z
x, −1/2+y, 3/2−z
1/2−x, 1−y, 1/2+z
1/2−x, 2−y, 1/2+z
Fig. 9 Relative energies (ΔE, kJ/mol) of title molecule crystallo-
graphic structure with (HAR) and without (CSD) Hirschfeld Atom
Refinement; DFT optimized structures
Fig. 7 Anisotropic H-atom placement by HAR (cf Fig. 2)
1 3

Journal of Chemical Crystallography
The columns are arranged in a staggered pattern, in two
dimensions, visible along the a axis (Fig. 5), and are held
together by the remaining three short contacts, tail-to-tail
H⋯F, and two head-to-head O⋯H (Fig. 6).
35] suite of programs. The in vacuo geometry optimisation
was followed by a frequency calculation, the absence of neg-
ative frequencies indicating that the optimised geometry was
at least a local minimum on the potential energy surface. The
relative energies [36] of the CSD, HAR, and DFT optimized
structures (OPT) are shown in Fig. 9, for the basis sets def2-
SVP and 6–31+G(d,p). For each basis set, the order of rela-
tive energies is the same, OPT<HAR<CSD.
Table 2 summarises the five short contacts with their
respective distances and symmetry operations.
Hirschfeld Refinement and DFT Simulation
Figure 10 illustrates the superposition using MacroModel
[18, 19] of the experimental and theoretical structures and
Table 4 shows the root-mean-square-deviation (RMSD)
between the structures, compared on an “all atoms” basis,
and the atom of maximum deviation.
Hirschfeld Atom Refinement (HAR) with Olex2 [13] using
the “Restricted Hartree–Fock” method with the def2-SVP
basis set [30–32] yields an improved R-factor of 1.5% and
anisotropic positioning of the hydrogen atoms (Fig. 7) with
longer bond lengths for C–H and O–H connections and
a single shorter O⋯H connection for the intramolecular
hydrogen bond. (Fig. 8; Table 3).
Table 5 contains relevant parameters for the structures
and Fig. 9 shows the relative energies.
The RMSD values (Table 4) indicate a relatively good
match between the structures although the structures pro-
duced by the in vacuo DFT simulations are more planar
and of lower energy, the greatest difference observed in the
inter-plane angle between the A and B rings (30° vs 2°–4°;
Table 5). Figure 11 illustrates this difference by superposi-
tion of the B-rings of the HAR and mPW1PW91/def2-SVP
structures. The non-planarity arises from rotation of two
bonds, C7–C8 and C9–C10, in the crystal structure.
The difference is attributed to the absence of the five
intermolecular interactions (Fig. 3) from the single-mole-
cule gas-phase simulation, particularly the hydrogen bonds
(Fig. 6) and the C–H⋯F interactions (Fig. 3) responsible
for the inter-column connections. In supermolecular archi-
tecture, hydrogen bonding is the prevalent interaction and,
while there is debate on whether the C–H⋯F interaction can
be termed a “hydrogen bond”, “weak hydrogen bond”, or a
Van der Waal’s interaction, this type of H⋯F interaction is
significant in the structure of crystals [37–39] It is notewor-
thy that while H4 and H12 (Table 4) do not feature in the
short contact interactions, H15 (Table 4) is a key feature of
the inter-column architecture of the crystal, in the C–H⋯F
interaction of 2.575 (1) Å [40].
Density functional theory (DFT) simulations of the
molecular geometry were performed for comparison with the
crystal structure, with and without HAR. The simulations
were carried out using the mPW1PW91 [33] functional and
the def2-SVP [30–32] basis set (used by the HAR in Olex2)
and the 6–31+G(d,p) basis set using the Gaussian-09 [34,
Fig. 10 Superposition (all atoms) of CSD (blue), HAR (green), OPT
mPW1PW91/def2-SVP (yellow), OPT mPW1PW91/6–31+G(d,p)
(magenta) structures
Table 4 RMSD values for structure comparisons (atom of maximum
difference)
The intramolecular H-bond (O2–H2⋯O1; Figs. 2, 7) is
reproduced by the DFT simulation (Fig. 12).
CSD
HAR
def2-SVP
CSD
HAR
def2-SVP
6–31+G(d,p)
–
0.0864 (H4)
–
0.3769 (H15)
0.3515 (H15)
0.3789 (H12)
0.3769 (H15)
–
0.0864 (H4)
0.3789 (H12)
0.3538 (H12)
0.0266 (H15)
Table 5 Selected structural
Parameter (°)
CSD
1.4
29.9
175.4
169.0
164.9
HAR
def2-SVP
6–31+G(d,p)
parameters
Interplane angle, S(6) and B-ring
Interplane angle, A and B rings
Torsion, C2–C1–C7–C8
Torsion C1–C7–C8–C9
Torsion, C8–C9–C10–C11
1.6
29.9
175.3
169.0
165.0
0.19
2.2
179.9
179.0
179.0
0.3
4.0
179.3
178.4
178.1
1 3

Journal of Chemical Crystallography
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