Cristallographic and conformational analysis of [(E)-2-[(3- chlorophenylimino)methy]-4-methoxyphenol]

Article abstract of DOI:10.1007/s10870-008-9483-y

The crystal structure of C₁₄H₁₂CINO₂ was determined by X-ray analysis. It crystallizes in the triclinic space group Pc with a = 12.5346(10) A, b = 4.5101(3) A, c = 12.0534(11) A, α = 90.00°, β = 113.669(6)°, γ = 90.00°, Z = 2, Dx = 1.393 mg/m³, μ (MoK_α) = 0.298 mm^-1. The title compound is photochromic and molecule is non-planar. It adopts a phenol-imine tautomeric form with a strong intramolecular C-H...N hydrogen bond and a strong intermolecular C-H...O hydrogen bond. Minimum energy conformations AMI were calculated as a function of the three torsion angles θ1(C10-C9-N1-C8), θ2(C9-N1-C8-C1) and θ3(N1-C8-C1-C6), varied every 10°. As in the X-ray experiment results, molecule has an angle that makes it non-planar between two aromatic rings in AM1 optimized geometry. Springer Science+Business Media, LLC 2008.

Full text of DOI:10.1007/s10870-008-9483-y

J Chem Crystallogr (2009) 39:353–357
DOI 10.1007/s10870-008-9483-y
ORIGINAL PAPER
Crystallographic and Conformational Analysis
of [(E)-2-[(3-Chlorophenylimino)methy])-4-methoxyphenol]
¨
˘
˘
Arzu Ozek Æ C¸ igdem Albayrak Æ Mustafa Odabas¸oglu Æ
¨
Orhan Bu¨yu¨kgu¨ngor
Received: 9 July 2007 / Accepted: 7 October 2008 / Published online: 23 October 2008
Ó Springer Science+Business Media, LLC 2008
Abstract The crystal structure of C14H12ClNO2 was
determined by X-ray analysis. It crystallizes in the triclinic
properties of Schiff bases which are photochromism and
thermochromism [3, 4]. These properties are caused by
proton transfer from hydroxyl O atom to the imine N
atom [5, 6]. It has been proposed that molecules showing
thermochromism are planar, while those showing photo-
chromism are non-planar [7]. In general, o-hydroxy Schiff
bases exhibit two possible tautomeric forms, the phenol–
imine (or benzenoid) and keto–amine (or quinoid) forms.
Depending on the tautomers, two types of intra-molecular
hydrogen bonds are possible: O–HÁÁÁN in benzenoid and
N–HÁÁÁO in quinoid tautomers. o-hydroxy Schiff bases have
been previously observed in the keto form [8], in the phenol
form[9] or in phenol/keto mixtures [10, 11].
˚
space group Pc with a = 12.5346(10) A, b = 4.5101(3) A,
˚
˚
c = 12.0534(11) A, a = 90.008, b = 113.669(6)8, c =
90.008, Z = 2, Dx = 1.393 mg/m3, l (MoKa) = 0.298
mm-1. The title compound is photochromic and molecule
is non-planar. It adopts a phenol–imine tautomeric form
with a strong intramolecular O–HÁÁÁN hydrogen bond and a
strong intermolecular C–HÁÁÁO hydrogen bond. Minimum
energy conformations AM1 were calculated as a function
of the three torsion angles h1(C10–C9–N1–C8), h2(C9–
N1–C8–C1) and h3(N1–C8–C1–C6), varied every 10°. As
in the X-ray experiment results, molecule has an angle that
makes it non-planar between two aromatic rings in AM1
optimized geometry.
Here we report the molecular and crystal structure
of (E)-2-[(3-chlorophenylimino)methy])-4-methoxyphenol
(Fig. 1), determined by single crystal X-ray diffraction
study, and the conformational analysis of the title molecule
with respect to the selected torsion angles are achieved by
AM1 semi-empirical quantum mechanical model.
Keywords Crystal structure Á Schiff base Á
Phenol–imine Á AM1 Á Conformational analysis
Introduction
Experimental
Most Schiff bases have antibacterial, anticancer, antin-
flammatory and antitoxic properties [1]. In addition to that,
Schiff bases have been used widely as ligands in the field of
coordination chemistry [2]. There are two characteristic
Synthesis of the Title Compound
The compound (E)-2-[(3-chlorophenylimino)methy])-4-
methoxyphenol was prepared byreflux a mixture of a
solution containing 5-methoxysalicylaldehyde (0.5 g
3.3 mmol) in 20 mL ethanol and a solution containing
3-chloraniline (0.420 g 3.3 mmol) in 20 mL ethanol.
The reaction mixture was stirred for 1 h under reflux.
The crystals of (E)-2-[(3-chlorophenylimino)methy])-4-
methoxyphenol suitable for X-ray analysis were obtained
from ethanol by slow evaporation (yield 82%; m.p. 346–
347 K).
¨
¨
A. Ozek (&) Á O. Bu¨yu¨kgu¨ngor
Department of Physics, Faculty of Arts and Sciences,
Ondokuz Mayıs University, Kurupelit, 55139 Samsun,
Turkey
e-mail: arzuozek@omu.edu.tr
˘
C¸ . Albayrak Á M. Odabas¸oglu
Department of Chemistry, Faculty of Arts and Sciences,
Ondokuz Mayıs University, Kurupelit, 55139 Samsun, Turkey
123

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J Chem Crystallogr (2009) 39:353–357
H3C
O
Table 1 Crystallographic data for the title compound
Color/shape
Brown/prism
C14H12ClNO2
Chemical formula
Formula weight
Temperature
261.70 akb
296 K
N
Crystal system
Space group
Monoclinic
Pc
O
H
´
Cl
˚
a = 12.5346(10) A
Unit cell parameters
´
˚
b = 4.5101(3) A
Fig. 1 Chemical diagram of the phenol–imine form for the title
compound
´
˚
c = 12.0534(11) A
a = 90.00°
b = 113.669(6)°
c = 90.00°
X-ray Crystallography
´
3
˚
A suitable sample of size 0.67 9 0.43 9 0.16 mm was
selected for the crystallographic study. All diffraction
measurements were performed at room temperature
(296 K) using graphite monochromated MoKa radiation
and an STOE IPDS 2 diffractometer. A total of 8,238
reflections with [3.39° \ h \ 27.49°] were collected in the
rotation mode and cell parameters were determined by
using X-AREA software [12]. Absorption correction
Volume
624.09(9) A
Z
2
Density
1.393 Mg m-3
0.298 mm-1
0.8367, 0.9516
STOE IPDS 2/--scan
3.39, 27.49°
8,238
Absorption coefficient
Tmin, Tmax
Diffractometer/meas. meth.
h range for data collection
Reflections read
(l = 0.298 mm-1
) was achieved by the integration
Unique reflections
5,464
method via X-RED software [12]. The structure was solved
by direct methods using SHELXS-97 [13]. The refinement
was carried out by full-matrix least-squares method on the
positional and anisotropic temperature parameters of the
non-hydrogen atoms, or equivalently corresponding to 212
crystallographic parameters. All non-hydrogen atom
parameters were refined anisotropically and all H atom
parameters were freely refined. The C–H distances are in
Data in refinement/restraints/parameters
Data with I [ 2r(I)
Goodness of fit on F2
R factor
2,848/2/212
2,848
1.041
0.0350
Weighted R factor
0.0970
Flack parameter
0.46(17)
˚
the range 0.88(3)–1.05(2) A and Uiso(H) values are in the
˚
range 0.052(6)–0.115(13) A [2].
squares (NLLSQ) gradient minimization routine was used
in the optimization procedure. To elucidate conformational
flexibility of the title molecule, the selected torsion angles
h1(C10–C9–N1–C8), h2(C9–N1–C8–C1) and h3(N1–C8–
C1–C6) are varied from 08 to 3608 in every 108 and the
molecular energies were calculated as a function of each h,
keeping the other h values constant thus molecular energy
profiles are obtained by performing single point calcula-
tions on the calculated potential energy surface. It is well
known that the AM1 and similar calculations underesti-
mate like inter- and intramolecular hydrogen bond
interactions. That is why, somewhat differences were
observed between X-ray experimental study and AM1
semi-empirical calculation results of bond distance, angle
and torsion angle values.
In the crystal structure, there is a twin by inversion
(racemic twin), as suggested by the value of the Flack
(1983) parameter of 0.46(17). The structure was refined to
R1 = 0.035 for observed reflections which obeyed to the
condition of 2,480 I [ 2r(I) and to R1 = 0.0970 for all
2,848 data used in refinement process. The maximum
peaks and deepest hole observed in the final Dq map were
0.163 and -0.201 eA-3, respectively. The scattering fac-
˚
tors were taken from SHELXL-97 [13]. The data collection
conditions and parameters of refinement process are listed
in Table 1.
Computational Procedure
The geometry optimization of the molecule leading to
energy minima was achieved by using AM1 semi-empiri-
cal quantum mechanical method [14] at the restricted
Hartree-Fock (RHF) level [15] with the aid of WinMopac
7.21 package [16]. Calculation was started from the crys-
tallographic coordinates of molecule. Non-Linear least
Results and Discussion
An ORTEP-3 plot [17] with the atom-numbering scheme
of the title compound is shown in Fig. 2. Comparative
results obtained from the X-ray crystallographic and
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J Chem Crystallogr (2009) 39:353–357
355
Fig. 2 An ORTEP view of the title compound with the atomic
numbering scheme. Dashed line shows intramolecular hydrogen
bond. Displacement ellipsoids are shown at the 30% probability level
Fig. 3 A partial packing view of the title compound shows the
formation of the C(5) chain through C–HÁÁÁO hydrogen bonds. H
atoms are represented as small spheres of arbitrary radii and H atoms
not involved in hydrogen bonding have been omitted for clarity
[symmetry code: (i) x, 1-y, z ? 1/2]
computational studies of bond distances, angles and torsion
angles are presented in Table 2.
In the title compound, the phenol–imine tautomer is
favoured over the keto-amine form, as indicated by the C2–
O1, C8–N1, C1–C8 and C1–C2 bond lengths (Fig. 2 and
Table 2). A similar work was observed for N-(2,5-meth-
˚
ylphenyl)salicylaldimine (C–O = 1.346(3) A, C–N =
˚
1.276(2) A) [18]. The H atom in the title compound is
˚
Table 3 Hydrogen bonding geometry (A, °) for the title compound
D–HÁÁÁA
D–H
HÁÁÁA
DÁÁÁA
D–HÁÁÁA
152 (4)
145.98 (2)
O1–H1ÁÁÁN1
0.75 (4)
1.01 (2)
1.95 (4)
2.633 (2)
3.382 (3)
C8–H8ÁÁÁO1i
2.494 (2)
Note: D donor, A acceptor. Symmetry code: (i) = x, 1-y, z ? 1/2
located on atom O1, thus confirming a preference for the
phenol–imine tautomer in the solid state. The C2–O1 bond
length indicate single-bond character, whereas the C8–N1
bond length is indicative of significant double-bond
character.
features. As is a common feature of o-hydroxysalicylidene
systems, title compound displays a strong intramolecular
hydrogen bond between atoms N1 and O1 [19, 20], and this
O1–H1ÁÁÁN1 hydrogen bond generates an S(6) ring motif
[21]. The crystal structure has a strong intermolecular
C–HÁÁÁO hydrogen bond. The occurence of C–HÁÁÁO
hydrogen bond results in the formation of C(5) chains
developing parallel to the c axis [22] (Fig. 3). Geometrical
parameters of the intra- and inter-molecular H-bonds are
listed in Table 3.
The dihedral angle between the C1–C6 and C9–C14
rings is 6.14(1)°. Against this background we can say that
the compound is non-planar and displays photochromic
˚
Table 2 Comparative results of the selected bond lengths (A), bond
and torsion angles (°)
In order to define the conformational flexibility of
compound, semi-empirical calculations using the AM1
X-ray
AM1
Bond lengths
C8–N1
1.278(2)
1.292
C2–O1
1.351(2)
1.451(2)
1.405(2)
1.414(2)
1.361(3)
1.368
1.466
1.408
1.4106
1.385
-9
-10
-11
-12
-13
-14
-15
C1–C8
C1–C2
N1–C9
C5–O2
Bond angles
C6–C5–02
C6–C1–C8
C9–N1–C8
C14–C9–N1
N1–C8–C1
C1–C2–O1
Torsion angles
C10–C9–N1–C8
C9–N1–C8–C1
N1–C8–C1–C6
115.69(18)
118.84(15)
120.51(13)
124.55(16)
122.70(14)
121.39(17)
114.851
116.139
121.685
123.373
123.804
125.819
100
θ1 (C10-C9-N1-C8) (o)
200
300
0
-173.45(15)°
-179.20(17)°
178.12(17)°
-148.696°
-179.091°
-177.946°
Fig. 4 Molecular energy profile against the selected torsional degree
h1 of freedom
123

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J Chem Crystallogr (2009) 39:353–357
2500
2000
1500
1000
500
h2(C9–N1–C8–C1) has an energy barrier at near 340°
because of steric interaction between H(C14) and H(O1).
There is a considerable energy difference (approximately
2,200 kcal/mol) between heat of formation values of the
most favorable and unfavorable conformer of the title
compound according to Fig. 5. This energy profile shows
that the cis-isomer around the N1–C8 double bond is
required great amount of energy, and corresponding to
unfavorable conformer. The energy profile as a function of
h3(N1–C8–C1–C6) shows two maxima at 80° and 280°
and a minima at near 180° (see Fig. 6).
0
-500
The planarity of molecule is controlled by h1, h2 and h3
torsion angles. The AM1 optimized geometry of the crystal
structure of title compound corresponding to non-planar
conformation is the most stable conformation which agrees
with the result obtained from X-ray investigation.
According to Bu¨rgi and Dunitz [23] the non-planarity of
N-benzylideneaniline and related compounds caused by
two principal factors: (a) the interaction of the ortho
hydrogen on the aniline ring and the hydrogen on the
bridge carbon is repulsive in the planar conformation but
reduced with increasing nonplanarity, (b) the p-electron
system, itself divisible into two components, including, on
the one hand, delocalisation between the –HC=N– double
bond and the aniline phenyl ring and, on the other hand,
delocalisation of the nitrogen lone pair electron of electrons
into the aniline ring which is essentially zero for the planar
conformation but increases with increasing non-planarity.
Consequently, the most stable conformation is primarily
determined by non-bonded hydrogen–hydrogen repulsions.
0
100
200
300
θ2 (C9-N1-C8-C1) (ο)
Fig. 5 Molecular energy profile against the selected torsional degree
h2 of freedom
-9
-10
-11
-12
-13
-14
-15
0
100
200
300
θ3(N1-C8-C1-C6) (ο)
Supplementary Material
Fig. 6 Molecular energy profile against the selected torsional degree
h3 of freedom
CCDC 653301 contains the supplementary crystallographic
data for this paper. These data can be obtained free of
charge via www.ccdc.cam.ac.uk/data_request/cif, by
e-mailing data_request@ccdc.cam.ac.uk, or by contacting
The Cambridge Crystallographic Data Centre, 12 Union
Road, Cambridge CB2 1EZ, UK; fax: ?44(0)1223-336033.
molecular orbital method were carried out. The calculated
molecular energy profiles of the molecule against the
selected torsional degrees of freedom are shown in Figs. 4–6.
The energy profiles show that the most stable conformation
is determined by non-bonded hydrogen-hydrogen repul-
sions. Some discrepancies between the molecular
conformations of the AM1 optimized structure (its heat of
formation is -14.263 kcal/mol) and the X-ray structure are
observed. According to X-ray crystallographic study
h1(C10–C9–N1–C8), h2(C9–N1–C8–C1) and h3(N1–C8–
C1–C6) torsion angles are -173.45(15)°, -179.20(17)°
and 178.12(17)°, same torsion angles are obtained as
-148.696°, -179.091° and -177.946° in the AM1 opti-
mized geometry of the title compound, respectively.
Acknowledgments The authors wish to acknowledge the Faculty of
Arts and Sciences, Ondokuz Mayıs University, Turkey, for the use of
the STOE IPDS 2 diffractometer (purchased under Grant F.279 of the
University Research Fund).
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