Conformation and structure of 3-methoxyphenyl-salicylaldimine

Article abstract of DOI:10.1016/S0022-2860(98)00897-7

3-methoxyphenyl-salicylaldimine (C₁₄H₁₃NO₂) was studied by X-ray analysis and AM1 molecular orbital methods. It crystallises in the monoclinic space group P2₁/c with a = 20.486(4) A, b = 4.7935(8) A A, c = 12.310(5) A, β = 107.43(2)°, V = 1153.3(6) A³, Z = 4, D₀ = 1.309 g cm^-3, Z = 4, and μ(MoK(α)) = 0.088 mm^-1. The structure was solved by direct methods and refined to R = 0.033 for 1635 reflections [I < 2((I)]. The title molecule was nearly planar. There was a strong intramolecular hydrogen bond of distance 2.598(2) A between the hydroxyl oxygen atom and imine nitrogen atom, the hydrogen atom essentially being bonded to the oxygen atom. Minimum energy conformations from AM1 were calculated as a function of the three torsion angles θ₁(C8-N1-C7-C6), θ₂(N1-C7-C6-C5), and θ₃(C9-C8-N1-C7) varied every 10°. The theoretical calculations were carried out to compare with experimental results of the molecular conformations. The optimized geometry of the crystal structure corresponding to a non-planar conformation is the most stable conformation in all theoretical calculations.

Full text of DOI:10.1016/S0022-2860(98)00897-7

Journal of Molecular Structure 484 (1999) 229–234
Conformation and structure of 3-methoxyphenyl-salicylaldimine
*
A. Elmali, M. Kabak , Y. Elerman
Department of Engineering Physics, Faculty of Sciences, University of Ankara, Besevler 06100, Ankara, Turkey
Received 15 August 1998; received in revised form 1 December 1998; accepted 1 December 1998
Abstract
3-methoxyphenyl-salicylaldimine (C14H13NO2) was studied by X-ray analysis and AM1 molecular orbital methods. It
˚
˚
˚
˚
crystallises in the monoclinic space group P21/c with a ˆ 20.486(4) A, b ˆ 4.7935(8) A A, c ˆ 12.310(5) A, b ˆ
107.43(2)Њ, V ˆ 1153.3(6) A , Z ˆ 4, D0 ˆ 1.309 g cm , Z ˆ 4, and m(MoKa ) ˆ 0.088 mmϪ1. The structure was solved by
3
-3
˚
direct methods and refined to R ˆ 0.033 for 1635 reflections [I Ͻ 2((I)]. The title molecule was nearly planar. There was a
˚
strong intramolecular hydrogen bond of distance 2.598(2) A between the hydroxyl oxygen atom and imine nitrogen atom, the
hydrogen atom essentially being bonded to the oxygen atom. Minimum energy conformations from AM1 were calculated as a
function of the three torsion angles u1(C8–N1–C7–C6), u2(N1–C7–C6–C5), and u3(C9–C8–N1–C7) varied every 10Њ. The
theoretical calculations were carried out to compare with experimental results of the molecular conformations. The optimized
geometry of the crystal structure corresponding to a non-planar conformation is the most stable conformation in all theoretical
calculations. ᭧ 1999 Elsevier Science B.V. All rights reserved.
Keywords: X-ray; Photochromism; Thermochromism; Schiff base; AM1
1. Introduction
molecular switches and the charge transport occurs
through overlapping intramolecular p-orbitals with
proton transfer [5].
Schiff bases were used extensively as ligands in the
field of coordination chemistry [1]. Some of the
reasons are that the intramolecular hydrogen bond
between the O and N atoms plays an important role
in the formation of metal complexes, and that Schiff
base compounds show photochromism and thermo-
chromism in the solid state by proton transfer from
the hydroxyl O atom to the imine N atom [2–4].
Proton transfer may also be a basis for the develop-
ment of molecular switches and the charge transport
occurs through overlapping intramolecular proton
transfer may also be a basis for the development of
On the basis of structural studies on photochromic
and thermochromic salicylideneaniline derivatives, it
was concluded that the significant difference lies in
the manner of the molecular packing in the lattice and
molecules exhibiting thermochromy are planar while
those exhibiting photochromy are non-planar [6].
With the aim of gaining a deep insight into the struc-
tural aspect responsible for the observed phenomenon
in the solid state, conformational and crystallographic
analysis of the title compound (I) has been carried
out and the results are presented in this paper. The
results were compared and predicate on the hypoth-
esis of the previous works which have thermo-
chromic and photochromic properties [7, and
references therein].
* Corresponding author. Fax: ϩ90-312-223-2395.
E-mail address: kabak@science.ankara.edu.tr (M. Kabak)
0022-2860/99/$ - see front matter ᭧ 1999 Elsevier Science B.V. All rights reserved.
PII: S0022-2860(98)00897-7

230
A. Elmali et al. / Journal of Molecular Structure 484 (1999) 229–234
Fig. 1. The molecular structure of the title compound. displacement ellipsoids are plotted at the 50% probability level [12].
2. Methods
respectively, for 158 parameters using the I values
of 1635 (I Ͻ 2s(I)) reflections. A weighting scheme
was used during the refinement as w ˆ 1/[s2(F02) ϩ
(0.0458P)2 ϩ 0.2153P] where P ˆ (F02 ϩ 2F02)/3. The
highest and lowest peak in the final difference map
The suitable crystals were obtained directly from
the synthesis of the compound. Solutions of 0.01 mol
of 3-methoxyaniline in 30 ml ethanol and 0.01 mol
salicylaldehyde in 50 ml ethanol were prepared
separately and then mixed. The precipitate which
separated from the solution was recrystallized for
2–3 d from Schiff base in 25 ml of dioxane solution.
Yellow prismatic crystals were formed during the
refluxions.
were 0.12 and –0.12 eAϪ3, respectively. Scattering
˚
factors were taken from SHELXL97 [9].
Crystal data for (I), C14H13NO2, Mr ˆ 227.3 g molϪ1
,
monoclinic P21/c, a ˆ 20.486(4), b ˆ 4.7935(8), c ˆ
3
˚
˚
12.310(5) A, b ˆ 107.43(2)Њ, V ˆ 1153.3(6) A , Z ˆ 4,
D0 ˆ 1.309 g cmϪ3 and m(MoKa) ˆ 0.088 mmϪ1
,
A crystal of dimensions 0.73 × 0.60 × 0.10 mm was
mounted on an Enraf-Nonius CAD-4 diffractometer
equipped with a graphite monochromator. Cell
constants were determined by least-squares refine-
ment of diffractometer angles for 25 reflections
collected in the range 1.04Њ Ͻ u Ͻ 25.78Њ. Three
standard reflections were monitored every 120 min,
but no considerable intensity variations were
recorded. A total of 3238 reflections were recorded,
with Miller indices hmin ˆ Ϫ 22, hmax ˆ 22, kmin ˆ 0,
kmax ˆ 5, lmin ˆ Ϫ 13, lmax ˆ 13. The structure was
solved by direct methods using SHELXS86 [8]. The
E-map computed from the phase set with the best
combined figure of merit revealed the positions of
all non-hydrogen atoms. Full-matrix least-square
refinement of the fractional coordinates of the non-
hydrogen atoms with anisotropic atomic displacement
parameters was performed SHELXL97[9]. Positions
of H atoms (except hydroxyl H atom) were centered at
calculated positions and refined using a riding model
for both positions and isotropic thermal parameters.
The hydroxyl H atom was found in the difference
Fourier maps calculated at the end of the refinement
process as a small positive electron density. Final
R(F) and wR(F2) factors were 0.033 and 0.094,
F(000) ˆ 480, T ˆ 292 K, R(F) ˆ 0.033 and
wR(F2) ˆ 0.094 for 1635 observed reflections. Flack
parameter was found to be zero in the refinement [10].
A list of structure factors, H atom fractional atomic
coordinates and anisotropic atomic displacement para-
meters for non-hydrogen atoms has been deposited with
the B.L.L.D. as SupplementaryPublicationsNo. SUP…
(13pp.).
Theoretical calculations were performed with the
semi-empirical quantum-mechanical program AM1
[11], which is part of the MOPAC package [12].
The X-ray geometry was optimized by using AM1
method. To determine the conformational energy
profiles, the optimized geometry was kept fixed, and
values of the AM1 energies were calculated as a func-
tions of the torsion angles u1(C8–N1–C7VC6),
u2(N1–C7–C6–C5) and u3(C9–C8–N1–C7) from
0Њ to 360Њ, varied every 10Њ. The results are illustrated
in Figs. 2–4. The molecular energies were calculated
as a function of each torsional angle (u), keeping the
other torsional angles constant. The optimized torsion
angles u1(C8–N1–C7–C6), u2(N1–C7–C6–C5) and
u3(C9–C8–N1–C7) of the title compound are
Ϫ7.94Њ, 9.08Њ and 134.24Њ, respectively. In all theore-
tical calculations it was found that the non-planar

A. Elmali et al. / Journal of Molecular Structure 484 (1999) 229–234
231
Fig. 2. AM1 calculated conformation energies for optimized X-ray of u1(C8–N1–C7–C6) torsion angle.
optimized conformation of X-ray structure was the
most stable conformation.
molecule C14 is the most deviated atom with the
0.12(2) A, respectively. The two Schiff base moieties
˚
[O1, C1–C7] and [N1, C8–C14, O2] are planar to
˚
within Ϫ 0.058(1) A (C14 atom) and are inclined at
an angle of 3.82(2)Њ. The whole molecule is not planar
for optimized molecule. The two Schiff base moieties
of optimized geometry [O1, C1–C7] and [N1, C8–
3. Results and discussion
Fractional atomic coordinates and equivalent
isotropic thermal parameters for non-hydrogen
atoms are given in Table 1. Bond distances and
bond angles are listed in Table 2. An ORTEP view
of the molecular structure of (I) is given in Fig.1 [13].
From some thermochromic and photochromic
Schiff base compounds it was proposed that molecules
exhibiting thermochromy are planar, while those
exhibiting photochromy are non-planar [6]. The title
molecule is nearly planar and from whole planar
˚
C14, O2] are planar to within 0.028(2) A (C14 atom)
and are inclined at an angle of 36.54(3)Њ). In (I) a
strong intramolecular hydrogen bond links O1 and
N1 atoms, the H atom being bonded to the O atom
(in Scheme 1).
The O1…N1, N1…H and O1–H bond distances are
˚
˚
˚
2.598(2) A, 1.72(2) A and 0.96(2) A, respectively, and
the bond angle of O1–H1…N1 is 150(2)Њ. The sum
˚
of the van der Waals radii of O and N [3.07 A] is
Fig. 3. AM1 calculated conformation energies for optimized X-ray of u2(N1–C7–C6–C5) torsion angle.

232
A. Elmali et al. / Journal of Molecular Structure 484 (1999) 229–234
Fig. 4. AM1 calculated conformation energies for optimized X-ray of u3(C9–C8–N1–C7) torsion angle.
significantly longer than the intramolecular O…N
hydrogen bond length [14]. The intramolecular
O1…N1 hydrogen bond length is comparable to
those observed for 2,20-azinodimethyldiphenol
[N1, C8–C14, O2] is 36.54(3)Њ in the optimized X-ray
structure. The molecular energy can be divided into
bonded and non-bonded contributions. The bonded
energy is considered to be independent of torsional
angle changes and therefore vanishes when relative
conformer energies are calculated. The non-bonded
energy (EN) is further separated into torsional (Eu ),
steric (ES) and electrostatic (EES) contributions.
˚
˚
2.611(6) A [5], N-benzylsalicylaldimine 2.587(5) A
[15], and for N-(5-bromsalicylidene)-2-aminopyri-
˚
˚
dene 2.581(6) A [16]. The N1–C7 1.280(2) A and
˚
O1–C1 1.350(2) A are consistent with the similar
compounds [17–20]. Besides the strong intramole-
cular affinity between O1 and N1 atoms in (I) there
EN ˆ Eu ϩ ES ϩ EES
;
ꢀ1†
are intermolecular
proximity between the
˚
H10A(i)…H13A(ii) (2.528(1) A), H9A(i)…H13A(ii)
where the torsional energy (Eu) is that part of the
(i)
(iii)
˚
˚
(2.781(1) A) and
(2.673(1) A), H11A …H14A
˚
Table 1
O2(i)…H14A(iv) (2.608(1) A) atoms, respectively.
The molecular planarity and the closest molecular
packing along the shortest crystal y-axis provide for
the title molecule is thermochromic [7, and rerfer-
ences therein] ((i): x, y, z; (ii): x, 0.5Ϫy, 0.5 ϩ z;
(iii): Ϫx, Ϫy, Ϫz; (iv): Ϫx, 0.5 ϩ y, Ϫ0.5Ϫz).
Atomic coordinates ( × 104) and equivalent isotropic displacement
parameters (A2 × 103). Ueq is defined as one-third of the trace of the
orthogonalized Uij tensor
x
y
z
Ueq
C(1)
C(2)
C(3)
C(4)
C(5)
C(6)
C(7)
N(1)
C(8)
C(9)
C(10)
C(11)
C(12)
C(13)
O(2)
C(14)
O(1)
3475(1)
3946(1)
4363(1)
4316(1)
3854(1)
3427(1)
2952(1)
2559(1)
2099(1)
2053(1)
1589(1)
1154(1)
1201(1)
1674(1)
806(1)
13716(3)
15654(4)
17028(4)
16514(4)
14591(3)
13135(3)
11099(3)
9677(3)
7660(3)
6859(3)
4874(4)
3635(3)
4410(3)
6390(3)
3344(3)
1458(4)
12417(3)
Ϫ7(1)
Ϫ133(2)
796(2)
1874(2)
2005(1)
1083(1)
1262(1)
445(1)
58(1)
74(1)
73(1)
67(1)
59(1)
49(1)
51(1)
51(1)
48(1)
61(1)
65(1)
59(1)
54(1)
53(1)
76(1)
78(1)
79(1)
In order to define the conformotional flexibility of
the title molecule, semi-empirical calculations using
the AM1 molecular method were carried out.
Although the X-ray structure is nearly planar, the
optimized structure of it is not planar. The angle
between two Schiff base moieties [O1, C1–C7] and
634(1)
1700(1)
1768(1)
811(1)
Ϫ244(1)
Ϫ322(1)
Ϫ1264(1)
Ϫ1247(2)
Ϫ935(1)
278(1)
3066(1)
Scheme 1.

A. Elmali et al. / Journal of Molecular Structure 484 (1999) 229–234
233
Table 2
Bond lengths (A) and angles (Њ)
and the hydrogen on the ‘bridge’ carbon, which is
repulsive in the planar conformation but is reduced
with the increasing non-planarity; and (b) the p-elec-
tron system, itself divisible into two components,
including, on the one hand, delocalization between
the –CHyN– double bond and the aniline phenyl
ring, (which is maximized for a planar conformation)
and, in contrast, delocalization of the nitrogen lone
pair electrons into the aniline ring which is essentially
zero for the planar conformation but increases with
increasing non-planarity (where the lone pair densiy
on the nitrogen may interact with the p-system of the
ring).
In summary, the AM1 optimized geometry of the
crystal structure of (I) which is bare and not influ-
enced from the other molecules (lack of the non-
bonded intermolecular repulsions) corresponding to
the non-planar conformation is the most stable confor-
mation in all considered calculations. The results
strongly indicate that the most stable conformation
is primarily determined by non-bonded hydrogen-
hydrogen repulsions. The interaction between the N
lone pair and the p-electrons of the rotated phenyl
ring, however, might also contribute to the conforma-
tional energy of (I).
˚
C(1)-O(1)
C(1)-C(2)
C(1)-C(6)
C(2)-C(3)
C(3)-C(4)
C(4)-C(5)
C(5)-C(6)
C(6)-C(7)
C(7)-N(1)
N(1)-C(8)
C(8)-C(13)
C(8)-C(9)
C(9)-C(10)
C(10)-C(11)
C(11)-C(12)
C(12)-O(2)
C(12)-C(13)
O(2)-C(14)
1.350(2)
1.381(2)
1.402(2)
1.374(2)
1.380(3)
1.365(2)
1.395(2)
1.441(2)
1.280(2)
1.417(2)
1.378(2)
1.397(2)
1.366(2)
1.381(2)
1.382(2)
1.372(2)
1.381(2)
1.415(2)
O(1)-C(1)-C(2)
O(1)-C(1)-C(6)
C(2)-C(1)-C(6)
C(3)-C(2)-C(1)
C(2)-C(3)-C(4)
C(5)-C(4)-C(3)
C(4)-C(5)-C(6)
C(5)-C(6)-C(1)
C(5)-C(6)-C(7)
C(1)-C(6)-C(7)
N(1)-C(7)-C(6)
C(7)-N(1)-C(8)
C(13)-C(8)-C(9)
C(13)-C(8)-N(1)
C(9)-C(8)-N(1)
C(10)-C(9)-C(8)
C(9)-C(10)-C(11)
C(10)-C(11)-C(12)
C(9)-C(10)-C(11)
C(10)-C(11)-C(12)
O(2)-C(12)-C(13)
O(2)-C(12)-C(11)
C(13)-C(12)-C(11)
C(8)-C(13)-C(12)
C(12)-O(2)-C(14)
119.5(1)
121.0(1)
119.5(2)
120.6(2)
120.7(2)
119.0(2)
122.0(2)
118.2(1)
120.2(1)
121.7(1)
122.4(1)
121.9(1)
118.6(1)
116.3(1)
125.2(1)
119.5(1)
122.1(2)
118.5(2)
122.1(2)
118.5(2)
115.3(1)
124.9(1)
119.9(1)
121.4(1)
117.9(1)
torsional energy which does not arrive from the steric
or electrostatic form. The energy profile as a function
of u1(C8–N1–C7–C6) shows one maxima near 10Њ
because of steric interactions between H(C7) and
hydroxyl H atoms. The energy profile as a function
of u2(N1–C7–C6–C5) has one maxima near 0Њ
because of steric interactions between H(C9) and
H(O1) atoms. The conformational energy as a func-
tion u3(C9–C8–N1–C7) shows a maxima near 320Њ
because of steric interactions between H(C13) and
H(C7) atoms. In the planar conformation the torsional
angles of u1(C8–N1–C7–C6), u2(N1–C7–C6–C5)
and u3(C9–C8–N1–C7) are 178.7(1)Њ, Ϫ 179.4(1)Њ
and 4.7(2)Њ, respectively and the planar conformation
is not the most stable conformation. The non-planar
conformation of (I) corresponding to the optimized X-
ray structure is the most stable conformation as shown
in Figs. 2–4. These results are in good agreement in
our previous works [21,22]. Burgi and Dunitz carried
out an extensive theoretical and experimental study on
the non-planar of N-benzylideneaniline involves a
competition between two principal factors: (a) the
interaction of the ortho hydrogen on the aniline ring
Acknowledgements
Financial support from the Scientific and Technical
Council of Turkey by project TBAG-1620 is grate-
fully acknowledged.
References
[1] M. Calligaris, L. Randaccio, in: G. Wilkinson (Ed.), Compre-
hensive Coordination Chemistry, 2, Pergamon, London, 1987,
pp. 715.
[2] M.D. Cohen, G.M.J. Schmidt, S. Flavian, J. Chem. Soc.
(1964) 2041–2051.
[3] M.D. Cohen, S. Flavian, J. Chem. Soc. (1967) 317–321.
[4] E. Hadjoudis, M. Vitterakis, I. Moustakali-Mavridis, Tetrahe-
dron 43 (1987) 1345–1360.
[5] X.-X. Xu, X.-Z. You, Z.-F. Sun, X. Wang, H.-X. Liu, Acta
Cryst. C50 (1994) 1169–1171.
[6] J. Bregman, L. Leiserowitz, G.M.J. Schmidt, J. Chem. Soc.
(1964) 2068.
[7] I. Moustakali-Mavridis, E. Hadjoudis, A. Mavridis, Acta
Cryst. B34 (1978) 3709–3715.
[8] G.M. Sheldrick, Acta Cryst. A46 (1990) 467–473.

234
A. Elmali et al. / Journal of Molecular Structure 484 (1999) 229–234
[17] Y. Elerman, I. Svoboda, H. Fuess, Z. Kristallogr. 196 (1991)
[9] G.M. Sheldrick, SHELXL97, Program for the Refinement of
¨
Crystal Structures, Univ. of Gottingen, Germany, 1997.
309–311.
[10] H.D. Flack, Acta Cryst. A39 (1983) 876–881.
[11] M.J.S. Dewar, E.G. Zeobisch, E.F. Healy, J.J.P. Stewart, J.
Am. Chem. Soc. 107 (1985) 3902–3909.
[12] J.P. Stewart, MOPAC Version 6.0, Quantum Chemistry
Program Exchange 581, Indiana Univ., USA, 1989.
[13] M.N. Burnett, C.K. Johnson, ORTEP, ORNL Report 6895,
1996.
[18] Y. Elerman, A. Elmali, M. Kabak, M. Aydin, M. Peder, J.
Chem. Cryst. 24 (1994) 603–606.
[19] Y. Elerman, A. Elmali, I. Svoboda, Acta Cryst. C51 (1995)
2344–2346.
¨
[20] A. Elmali, S. Ozbey, E. Kendi, M. Kabak, Y. Elerman, Acta
Cryst. C51 (1995) 1878–1880.
[21] A. Elmali, Y. Elerman, C.T. Zeyrek, J. Mol. Struc. 443 (1998)
[14] A. Bondi, J. Phys. Chem. 68 (1964) 441–451.
[15] Y. Elerman, H. Paulus, I. Svoboda, H. Fuess, Z. Kristallogr.
198 (1992) 135–136.
123–130.
[22] M. Kabak, A. Elmali, Y. Elerman, J. Mol. Struc., (1998) (In
press).
[16] I. Moustakali-Mavridis, E. Hadjoudis, Acta Cryst. A46 (1978)
467–473.